File: gpp.rtf ============== 31 1 !Modified by Efrat Pahima December 2017 to match with the Resorcinarene !supramolecular capsule, of prof. Tiefenbacher K.'s group RESI GPP -3 GROUP ATOM C2 CE1 -0.33 ATOM H21 HE1 0.22 ATOM C3 CE 0.11 GROUP ATOM C4 CT2 -0.18 ATOM H41 HA 0.09 ATOM H42 HA 0.09 GROUP ATOM C5 CT2 -0.18 ATOM H51 HA 0.09 ATOM H52 HA 0.09 GROUP ATOM C6 CE1 -0.33 ATOM H61 HE1 0.22 ATOM C7 CE 0.11 GROUP ATOM C8 CT3 -0.27 ATOM H81 HA 0.09 ATOM H82 HA 0.09 ATOM H83 HA 0.09 GROUP ATOM C9 CT3 -0.27 ATOM H91 HA 0.09 ATOM H92 HA 0.09 ATOM H93 HA 0.09 GROUP ATOM C10 CT3 -0.27 ATOM H101 HA 0.09 ATOM H102 HA 0.09 ATOM H103 HA 0.09 GROUP ATOM C1 CN8 0.08 !-0.08 ATOM H11 HN8 0.09 ATOM H12 HN8 0.09 ATOM O1 ON2 -0.51 !-0.62 GROUP ATOM P1 P 1.5 ATOM O2 ON3 -0.82 ATOM O3 ON3 -0.82 ATOM O4 ON2 -0.74 ATOM P2 P2 1.1 ATOM O5 ON3 -0.9 ATOM O6 ON3 -0.9 ATOM O7 ON3 -0.9 BOND C1 O1 C1 C2 C2 H21 BOND C1 H11 C1 H12 BOND C3 C4 C4 H41 C4 H42 BOND C4 C5 C5 H51 C5 H52 C5 C6 BOND C6 H61 C7 C8 C8 H81 C8 H82 BOND C8 H83 C7 C9 C9 H91 C9 H92 BOND C9 H93 BOND C3 C10 C10 H101 C10 H102 C10 H103 BOND O1 P1 P1 O2 P1 O3 P1 O4 BOND P2 O4 P2 O5 P2 O6 P2 O7 DOUBLE C2 C3 C6 C7 RESI CLA -1.00 ! Chloride Ion GROUP ATOM CLA0 CLA -1.00 PATCHING FIRST NONE LAST NONE RESI HCL 1.00 ! Proton, positive hydrogen GROUP ATOM HCL HCL 1.00 PATCHING FIRST NONE LAST NONE PRES ACE 0.00 ! acetylated N-terminus (top_all36_prot.rtf) ! modified to match the GOAc -> turning GPP into GOAc! (by Efrat) GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY CD 0.75 !0.51 CY=OY ATOM OY OB -0.50 !-0.51 | ! O1 DELETE ATOM P1 DELETE ATOM O2 DELETE ATOM O3 DELETE ATOM O4 DELETE ATOM P2 DELETE ATOM O5 DELETE ATOM O6 DELETE ATOM O7 BOND CY CAY CY O1 CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY O1 OY ACCEPTOR OY CY IC CY O1 C1 C2 0.0000 0.0000 -60.0000 0.0000 0.0000 !IC CY C1 *O1 HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY O1 C1 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 END File: gpp.prm ============== *>>>>>> Additional parameters for GPP and deprotonated PPi <<<<<< *>>> To be used with the CHARMM22 All-Hydrogen Parameter File <<< *>>>>>>>>>>>>> for Proteins and Nucleic Acids <<<<<<<<<<<<<<<<<<< ! From: ! Marc W. van der Kamp, Jitnapa Sirirak, Jolanta Zurek, Rudolf K. ! Allemann and Adrian J. Mulholland. Conformational change and ! ligand binding in the aristolochene synthase catalytic cycle. ! ! !Modified by Efrat Pahima December 2017 to match with the Resorcinarene !supramolecular capsule, of prof. Tiefenbacher K.'s group ! BONDS CT3 CE 248.8 1.51 CT2 CE 217.9 1.51 CE1 CN8 244.0 1.51 CE CE1 433.9 1.35 !ON4 P2 277.5 1.58 !!For GPP as well!! HE1 CE1 360.500 1.1000 ! ! for propene, yin/adm jr., 12/95 CN8 HN8 309.0 1.111 !Alkanes, sacred CE1 CT2 365.000 1.5020 ! ! for butene; from propene, yin/adm jr., 12/95 CT2 CT2 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 222.500 1.5280 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CE1 CE1 440.000 1.3400 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CT3 383.000 1.5040 ! ! for butene, yin/adm jr., 12/95 CN8 ON2 340.0 1.44 ! !!for GOAc -patching the "acetylated N-terminus" (top_all36_prot.rtf) and GPP!! !!using par_all36_lipid.prm, CL=CD, OBL=OB, OSL=OS=ON2, CTL2=CT2=CN8, HAL=HA=HN8 CT3 CD 200.0 1.522 ! CAY (methyl carbon) to CY (carbonyl carbon) OB CD 750.0 1.220 ! OY (carbonyl oxygen) to CY (carbonyl carbon) ON2 CD 150.0 1.334 ! O1 (acetate oxygen) to CY (carbonyl carbon) !!For LOAc!! CE1 CE2 500.000 1.3420 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 365.000 1.1000 ! ! for ethene, yin/adm jr., 12/95 CN8 CT3 383.000 1.5040 ! ! for butene, yin/adm jr., 12/95 CN8 CT2 365.000 1.5020 ! ! for butene; from propene, yin/adm jr., 12/95 ANGLES HA CT3 CE 31.8 111.4 HA CT2 CE 35.2 109.3 HE1 CE1 CE 17.4 118.2 CT3 CE CT3 26.9 118.9 CT3 CE CT2 34.0 120.1 CT3 CE CE1 49.9 121.4 CT2 CT2 CE1 32.0 112.2 CT2 CT2 CE 32.0 112.2 CT3 CT2 CE 15.2 113.1 CT2 CE1 CE 55.5 126.6 CT2 CE CE1 39.8 115.3 CE CE1 CN8 67.6 128.2 HE1 CE1 CN8 54.2 112.1 CE1 CN8 HN8 6.1 110.2 CE1 CN8 ON2 48.1 110.8 !!For GPP as well!! HE1 CE1 CE1 52.00 119.50 ! ! for 2-butene, yin/adm jr., 12/95 HE1 CE1 CT2 40.00 116.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HE1 CE1 CT3 22.00 117.00 ! ! for propene, yin/adm jr., 12/95 HN8 CN8 CN8 34.53 110.10 22.53 2.179 ! HN8 CN8 HN8 35.5 109.00 5.40 1.802 ! HN8 CN8 ON2 60.0 109.5 !DMP, adm jr. CE1 CE1 CT2 48.00 123.50 ! ! for 2-butene, yin/adm jr., 12/95 CE1 CE1 CT3 48.00 123.50 ! ! for 2-butene, yin/adm jr., 12/95 CE1 CT2 CT3 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CE1 45.00 111.50 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CE1 42.00 111.50 ! ! for 2-butene, yin/adm jr., 12/95 HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 !!for GOAc -patching the "acetylated N-terminus" (top_all36_prot.rtf) and GPP!! using par_all36_lipid.prm !!par_all36_prot.prm ON2 CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate !!par_all36_lipid.prm, CL=CD, OBL=OB, OSL=OS=ON2, CTL2=CT2=CN8, HAL=HA=HN8 OB CD CT3 70.0 125.0 20.0 2.442 ! methyl acetate CD ON2 CN8 40.0 109.6 30.0 2.2651 ! methyl acetate HA CT3 CD 33.00 109.50 30.00 2.163 ! methyl acetate ON2 CD CT3 55.0 109.0 20.00 2.3260 ! methyl acetate !!!!For LOAc!!! from par_all36_prot.prm , par_all36_lipid.prm ON2 CN8 CT3 65.000 122.0000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 ON2 CN8 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 HE1 CE1 CE2 42.00 118.00 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE1 45.00 120.50 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 HE2 19.00 119.00 ! ! for propene, yin/adm jr., 12/95 CN8 CE1 CE2 67.6 128.2 CE1 CN8 CT3 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE1 CN8 CT2 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CT3 CN8 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CN8 26.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CN8 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CT2 CN8 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) DIHEDRAL HA CT2 CE1 CE 0.3 3 0.0 HA CT3 CE1 CE 0.1 3 0.0 HA CT3 CE CE1 0.5 3 0.0 HA CT3 CE CT3 0.5 3 0.0 HA CT3 CE1 CT3 0.5 3 0.0 HA CT3 CE CT2 0.5 3 0.0 HA CT2 CE CE1 0.1 3 0.0 HA CT2 CE CT3 0.8 3 180.0 CT3 CE1 CE CT3 5.2 2 180.0 CT3 CE CE1 CT2 2.6 2 180.0 CT2 CE CE1 CT2 5.0 2 0.0 CT2 CT2 CE1 CE 0.1 3 180.0 CT3 CT2 CE1 CE 0.04 3 180.0 CT3 CT2 CE CE1 0.4 3 0.0 CT2 CT2 CE CE1 0.1 3 180.0 CT2 CT2 CE CT3 0.5 3 180.0 CT3 CT2 CE CT3 0.45 3 0.0 HE1 CE1 CE CT3 2.6 2 180.0 HE1 CE1 CT2 CT2 0.12 3 0.0 HE1 CE1 CE CT2 4.2 2 180.0 CT2 CE CE1 CN8 5.2 2 180.0 CT3 CE CE1 CN8 5.2 2 180.0 CE CE1 CN8 HN8 0.2 3 180.0 CE CE1 CN8 ON2 0.9 3 180.0 CE1 CN8 ON2 P 4.6 3 180.0 HE1 CE1 CN8 HN8 0.1 3 180.0 HE1 CE1 CN8 ON2 0.04 3 180.0 !!For GPP as well!! HE1 CE1 CE1 HE1 1.0000 2 180.00 ! ! 2-butene, adm jr., 8/98 update CT3 CE1 CE1 HE1 1.0000 2 180.00 ! ! 2-butene, adm jr., 8/98 update HE1 CE1 CT2 HA 0.0000 3 0.00 ! butene, adm jr., 2/00 update HE1 CE1 CT2 CT3 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CT3 HA 0.0000 3 0.00 ! butene, adm jr., 2/00 update CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI ! rotation barrier in Ethane (SF) CE1 CE1 CT3 HA 0.0300 3 0.00 ! ! for butene, yin/adm jr., 12/95 X CE1 CE1 X 0.1500 1 0.00 ! 2-butene, adm jr., 2/00 update X CE1 CE1 X 8.5000 2 180.00 ! 2-butene, adm jr., 2/00 update X CN8 ON2 X -0.10 3 0.0 ! phosphate ester X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) !!for GOAc -patching the "acetylated N-terminus" (top_all36_prot.rtf) and GPP!! using par_all36_lipid.prm !par_all36_lipid.prm, CL=CD, OBL=OB, OSL=OS=ON2, CTL2=CT2=CN8, HAL=HA=HN8 OB CD ON2 CN8 0.9650 1 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD ON2 CN8 3.8500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CD ON2 X 2.0500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate !!FOR LOAc!!!from par_all36_lipid HE1 CE1 CE2 HE2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 HE2 CE2 CE1 CN8 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 CE1 CN8 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 CE1 CN8 CT3 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HE1 CE1 CN8 CT3 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 HE1 CE1 CN8 CT2 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CN8 CT3 0.9100 1 180.0 !2-hexene, adm jr., 11/09, end fix jbk CE2 CE1 CN8 CT3 0.1800 2 180.0 !2-hexene, adm jr., 11/09 CE2 CE1 CN8 CT3 0.1700 3 180.0 !2-hexene, adm jr., 11/09 CE2 CE1 CN8 CT2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 CE2 CE1 CN8 CT2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 CE2 CE1 CN8 CT2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 X CE1 CE2 X 0.4500 1 180.00 ! 2-butene, adm jr., 4/04 X CE1 CE2 X 8.5000 2 180.00 ! CE1 CN8 CT2 CT2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 CE1 CN8 CT2 CT2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 CE1 CN8 CT2 CT2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 CE1 CT2 CT2 CN8 0.1400 1 180.0 !2-hexene, adm jr., 11/09 CE1 CT2 CT2 CN8 0.1700 2 0.0 !2-hexene, adm jr., 11/09 CE1 CT2 CT2 CN8 0.0500 3 180.0 !2-hexene, adm jr., 11/09 X CN8 CT3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell CT3 CN8 CT2 HA 0.060 2 0.00 ! alkane, 7/08, jbk CT3 CN8 CT2 HA 0.035 5 0.00 ! alkane, 7/08, jbk CT2 CT2 CN8 CT3 0.162 2 0.00 ! alkane, 7/08, jbk CT2 CT2 CN8 CT3 0.047 3 180.00 ! alkane, 7/08, jbk CT2 CT2 CN8 CT3 0.105 4 0.00 ! alkane, 7/08, jbk CT2 CT2 CN8 CT3 0.177 5 0.00 ! alkane, 7/08, jbk HA CT2 CN8 ON2 0.000 3 0.00 ! glycerol, theta3 CT2 CT2 CN8 ON2 0.000 3 0.00 ! glycerol, theta3 CE2 CE1 CN8 ON2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update CE2 CE1 CN8 ON2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update IMPROPER OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL ! adm jr., 10/17/90, acetic acid vibrations CD CT3 OB OH1 0.000 0 0.00 !added by Efrat HE2 HE2 CE2 CE2 3.0 0 0.00 ! ! for ethene, yin/adm jr., 12/95 NONBONDED !In the icap.prm file! END File: icap.rtf ============== *>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<< *>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<< *>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< *>>>>>>>>>>>>>>>>>>>>>> July, 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * 31 1 ! references ! !PROTEINS ! !MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the !treatment of backbone energetics in protein force fields: limitations !of gas-phase quantum mechanics in reproducing protein conformational !distributions in molecular dynamics simulations, Journal of !Computational Chemistry, 25: 1400-1415, 2004. ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. ! !IONS (see lipid and nucleic acid topology and parameter files for !additional ions ! ! ! ! !Modified by Efrat Pahima August 2017 to match with the Resorcinarene !supramolecular capsule !Atomic Mass for each atom type:! MASS 1 H 1.00800 H ! polar H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS -1 HCM 1.00800 H ! Chloroform MASS -1 CLCM 35.45000 Cl! Chloroform MASS -1 CCM 12.01100 C ! Chloroform MASS 11 HE1 1.00800 H ! for alkene; RHC=CR !GPP MASS -1 HE2 1.00800 H ! for alkene; RHC=CR !LOAc MASS -1 HN8 1.00800 H ! GPP MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 !GPP MASS 39 CE1 12.01100 C ! for alkene; RHC=CR !GPP MASS -1 CE2 12.01100 C ! for alkene; RHC=CR !LOAc MASS -1 CE 12.01100 C ! GPP MASS -1 CN8 12.01100 C ! GPP MASS -1 ON2 15.99900 O ! GPP MASS -1 OB 15.99900 O ! carbonyl oxygen !GOAc MASS -1 CD 12.01100 C ! carbonyl C !GOAc MASS 105 CLA 35.450000 CL ! Chloride Ion MASS -1 HCL 1.00800 H ! Proton DECL -CG2 DECL -CD1 !!*prescribes which atoms will be selected from the previous or next residue when covalently linking residue together* DECL +CB DECL +CG1 DEFA FIRS none LAST none AUTO ANGLES DIHE !!*AUTO ANGLes specifies that all possible angles and DIHEdral specifies that all possible dihedral angles be generated when building a structure.* !***RESIDUES***! RESI TIP3 0.000 ! *will be required for generating the 8 water molecules in the capsule*! GROUP ! tip3p water model, generate using noangle nodihedral ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake ANGLE H1 OH2 H2 ! required DONOR H1 OH2 DONOR H2 OH2 ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI RSR1 0.00 ! *Aromatic-Ring unit that construct the Resorcinarene(RSR) monomer (4 RSR1 are one Resorcinarene-RSR monomer)* GROUP ! ATOM CB CT1 -0.09 ! HD1 +CB ATOM HB HA 0.09 ! \ | GROUP ! HB CD1--CG2 ATOM CG1 CA 0.00 ! \ | // \\ ATOM CD1 CA -0.115 ! HF2 CB---CG1 CZ1--OH1 ATOM HD1 HP 0.115 ! \ / \ __ / \ GROUP ! HF1--CF CZ2--CD2 HH1 ATOM CG2 CA 0.00 ! | | \ GROUP ! HF3 OH2 HD2 ATOM CZ1 CA 0.11 ! \ ATOM OH1 OH1 -0.54 ! HH2 ATOM HH1 H 0.43 ! GROUP ! ATOM CD2 CA -0.115 ! ATOM HD2 HP 0.115 ! GROUP ! ATOM CZ2 CA 0.11 ! ATOM OH2 OH1 -0.54 ! ATOM HH2 H 0.43 ! GROUP ! ATOM CF CT3 -0.27 ! ATOM HF1 HA 0.09 ! ATOM HF2 HA 0.09 ! ATOM HF3 HA 0.09 ! BOND CG1 CB CZ2 CG1 CZ1 CD2 CG2 CD1 BOND OH1 CZ1 OH2 CZ2 CG2 +CB !*the (+) means CG2 is connected to the NEXT CB in line!* BOND CD1 HD1 CD2 HD2 OH1 HH1 OH2 HH2 BOND CB HB CB -CG2 CF CB BOND CF HF1 CF HF2 CF HF3 DOUBLE CD2 CZ2 CG2 CZ1 CD1 CG1 DONOR HH1 OH1 DONOR HH2 OH2 ACCEPTOR OH1 !!*there are two options for acceptor antecedent (CZ1, HH1) and not one, thus this Oxygene is written by himself!!* ACCEPTOR OH2 IC -CD1 -CG2 CB CG1 1.3942 122.6000 -85.5290 112.9400 1.5113 IC CG1 -CG2 *CB CF 1.5258 111.9600 127.4850 112.2960 1.5346 IC CG1 -CG2 *CB HB 1.5258 111.9600 -117.1070 107.0230 1.0952 IC -CG2 CB CG1 CD1 1.5234 111.9600 87.3870 121.5290 1.3963 IC CD1 CB *CG1 CZ2 1.3963 121.5290 179.3060 121.1450 1.4046 IC CB CG1 CD1 CG2 1.5258 121.5290 177.3280 123.9150 1.3942 IC CG2 CG1 *CD1 HD1 1.3942 123.9150 -179.0460 118.1490 1.0868 IC CB CG1 CZ2 CD2 1.5258 121.1450 -176.8670 120.3540 1.3949 IC CD2 CG1 *CZ2 OH2 1.3949 120.3540 178.1170 123.6220 1.3583 IC CD2 CZ2 OH2 HH2 1.3949 116.0000 -156.1430 111.3950 0.9719 IC CG1 CD1 CG2 CZ1 1.3963 123.9150 0.3210 116.5630 1.3973 IC CZ1 CD1 *CG2 +CB 1.3973 116.5630 179.4670 122.6000 1.5234 IC CZ1 CG2 +CB +CG1 1.3973 120.8350 93.9160 111.9600 1.5258 IC CZ1 CZ2 *CD2 HD2 1.3867 120.0630 -179.4440 118.4120 1.0866 IC CG2 CD2 *CZ1 OH1 1.3973 121.7380 -179.7220 120.7120 1.3808 IC CG2 CZ1 OH1 HH1 1.3973 117.5500 -177.8660 110.0160 0.9641 IC CG1 HB *CB CF 1.5258 107.1340 -119.9410 105.5760 1.5346 IC -CG2 CF *CB HB 1.5234 112.2960 -116.2810 105.5760 1.0952 IC HF2 CB *CF HF1 1.0930 112.8430 119.9870 109.8910 1.0933 IC HF1 CB *CF HF2 1.0933 109.8910 -119.9870 112.8430 1.0930 IC CD1 CG1 CB CF 1.3963 121.5290 -40.0660 112.3540 1.5346 IC CF CG1 *CB -CG2 1.5346 112.3540 127.4540 111.9600 1.5234 IC -CG2 CG1 *CB HB 1.5234 111.9600 117.0410 107.1340 1.0952 IC CG1 CB CF HF1 1.5258 112.3540 -175.3720 109.8910 1.0933 IC HF2 CB *CF HF3 1.0930 112.8430 -120.1040 109.9720 1.0933 IC HF1 HF2 *CF HF3 1.0933 107.5210 -117.1840 107.5680 1.0933 RESI CCL3 0.000 !Chloroform! GROUP ATOM C CCM 0.179 ATOM CL01 CLCM -0.087 ATOM CL02 CLCM -0.087 ATOM CL03 CLCM -0.087 ATOM HX HCM 0.082 BOND C CL01 C CL02 C CL03 C HX BOND CL01 CL02 CL01 CL03 !for shake BOND CL01 HX CL02 HX CL03 HX ! for shake ANGLE HX C CL01 HX C CL02 HX C CL03 ANGLE CL01 C CL02 CL01 C CL03 CL02 C CL03 PATCHING FIRS NONE LAST NONE PRES CYCL -0.275! *PATCH for connecting two RSR1 units to form the RSR monomer! (4 RSR1 are one Resorcinarene-RSR monomer)* GROUP ! ATOM 1CB CT1 -0.09 ! ATOM 1HB HA 0.09 ! __ / \ ATOM 1CG1 CA 0.00 ! -- CG1--2CD1 CD1--CG2 -- ATOM 1CF CT3 -0.27 ! / \ // \\ GROUP ! --CZ2 2CG2 1HB 1CG1 CZ1-- ATOM 2CG2 CA 0.00 ! \\ // \ | / \ __ / ATOM 2CD1 CA -0.115! CD2--2CZ1 1CB CZ2--CD2 ATOM 2CZ1 CA 0.11 ! / \ | | \ ! 1CF ! /| \ ! HF2 HF1 HF3 ! ! BOND 1CB 2CG2 IC 1CF 1CG1 *1CB 2CG2 1.5346 112.3540 127.4540 111.9600 1.5234 IC 2CG2 1CF *1CB 1HB 1.5234 112.2960 -116.2810 105.5760 1.0952 IC 2CZ1 2CG2 1CB 1CG1 1.3973 120.8350 93.9160 111.9600 1.5258 IC 2CD1 2CZ1 *2CG2 1CB 1.3942 116.5630 -179.4770 120.8350 1.5234 !IC 2CG2 1CB 1CG1 1CD1 1.5234 111.9600 87.3870 121.5290 1.3963 PATCH FIRST NONE LAST NONE !!*no need (used when DEFA is to be overridden)* END File: icap.prm ============== *>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<< *>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<< *>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< *>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * ! references ! !PROTEINS ! !MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the !treatment of backbone energetics in protein force fields: limitations !of gas-phase quantum mechanics in reproducing protein conformational !distributions in molecular dynamics simulations, Journal of !Computational Chemistry, 25: 1400-1415, 2004. ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. ! ! !Modified by Efrat Pahima August 2017 to match with the Resorcinarene !supramolecular capsule, of prof. Tiefenbacher K.'s group ! BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! CA CA 305.000 1.3750 ! ALLOW ARO ! benzene, JES 8/25/89 CT1 CA 230.000 1.4900 ! ALLOW ALI ARO !!*EDITED BY EFRAT to match with the resorcinarene capsule*! same as below (TYR) ! phe,tyr, JES 8/25/89 !! CT1=CT2 CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HP CA 340.000 1.0800 ! ALLOW ARO ! phe,tyr JES 8/25/89 HT HT 0.000 1.5139 ! ALLOW WAT ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) OH1 CA 334.300 1.4110 ! ALLOW ARO ALC ! MeOH, EMB 10/10/89, OH1 H 545.000 0.9600 ! ALLOW ALC ARO ! EMB 11/21/89 methanol vib fit OT HT 450.000 0.9572 ! ALLOW WAT ! FROM TIPS3P GEOM CCM CLCM 500.0 1.758 !Chloroform! from: toppar_chloroform_dh.str CCM HCM 500.0 1.100 !Chloroform! from: toppar_chloroform_dh.str CLCM CLCM 0.0 2.9028314 !Chloroform! from: toppar_chloroform_dh.str HCM CLCM 0.0 2.3383924 !Chloroform! from: toppar_chloroform_dh.str ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! ! CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO ! JES 8/25/89 CA CT1 CA 52.000 108.0000 ! ALLOW ALI ARO *!* EDITED BY EFRAT 11/17 CA=CT1 CT2=CT1 to fit with the resorcinarene capsule ! PARALLH19 (JES) CT1 CA CA 45.800 120.0000 ! ALLOW ALI ARO *!* EDITED BY EFRAT 11/17 to fit with resorcinarene capsule, same as TYR bellow CT1=CT2 ! PARALLH19 (JES) !CT3 CT1 CA 52.000 108.0000 ! ALLOW ALI PEP POL ARO !*EDITED BY EFRAT to fit rsr 11/17* same as CA=C bellow* ! ! Alanine Dipeptide ab initio calc's (LK) CT3 CT1 CA 51.800 107.5000 ! ALLOW ALI ARO ^ ANOTHER OPTION !!EDITED BY EFRAT ! ethylbenzene, adm jr., 3/7/92 H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO ! JES 8/25/89 phenol HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CA 49.300 107.5000 ! *EDITED BY EFRAT 09/17 TO FIT RSR* !similar to HA-CT2-CA of TYR HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO ! JES 8/25/89 benzene HT OT HT 55.000 104.5200 ! ALLOW WAT ! TIP3P GEOMETRY, ADM JR. OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC ! PARALLH19 WITH [122.3] (JES) CLCM CCM CLCM 0.0 111.30 !Chloroform! from: toppar_chloroform_dh.str HCM CCM CLCM 0.0 107.57 !Chloroform! from: toppar_chloroform_dh.str DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 CA CT1 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI !*EDITED BY EFRAT to match with the resorcinarene capsule*! same as below (TYR) ! ethylbenzene ethyl rotation, adm jr. 3/7/92 !*CT1=CA , CT2=CT1 CT1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO !*EDITED BY EFRAT to match with the resorcinarene capsule (TYR) same as below ! JES 8/25/89 toluene and ethylbenzene !*CT1=CT2 CT3 CT1 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI !*EDITED BY EFRAT to match with the resorcinarene capsule, same as below ! ethylbenzene ethyl rotation, adm jr. 3/7/92 !*CT1=CT2 H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 HA CT1 CA CA 0.0000 3 0.00 ! ALLOW ARO !!*EDITED BY EFRAT to match with the resorcinarene capsule, same as below ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 !! (HIS) CT1=CT2, CA=CPH1 HA CT3 CT1 CA 0.0400 3 0.00 ! ALLOW ARO !!EDITED BY EFRAT ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene OH1 CA CA CT1 4.2000 2 180.00 ! ALLOW ARO !!*EDITED BY EFRAT to match with the resorcinarene capsule, same as below ! JES 8/25/89 toluene and ethylbenzene !! FIRST OPTION : (TYR) OH1=HP, CT1=CT2 ! !CT1 CA CA CT1 0.2000 3 0.00 !! SECOND OPTION : FROM: par_all36_carb.prm, monosacharids !CC321 CC3163 CC3161 OC311 0.20 3 0.0 ! ^ ! HP CA CA CT1 2.0000 2 180.00 ! ALLOW ARO !!*EDITED BY EFRAT to match with the resorcinarene capsule, same as below ! adm jr., 3/24/92, maintain old aliphatic H VDW params !! (HIS) HP=HR3 , CA=CPH1, CT1=CT2 OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 !X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CCM CLCM CLCM CLCM 0.000 0 0.00 CCM CLCM CLCM HCM 0.000 0 0.00 CMAP ! 2D grid correction data. The following surfaces are the correction ! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces. ! Use of CMAP requires generation with the topology file containing the ! CMAP specifications along with version 31 or later of CHARMM. Note that ! use of "skip CMAP" yields the charmm22 energy surfaces. ! ! references !MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of !Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted !for publication. !MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the !Protein Backbone in Empirical Force Fields, Journal of the American Chemical !Society, In Press. NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - !cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! CA 0.000000 -0.070000 1.992400 ! ALLOW ARO ! benzene (JES) CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 ! hydrogens H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy HT 0.000000 -0.046000 0.224500 ! ALLOW WAT !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete ! oxygens OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) OT 0.000000 -0.152100 1.768200 ! ALLOW WAT !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete !Chloroform! CCM 0.0 -0.102 1.9082 ! CLCM 0.0 -0.300 1.9306 ! HCM 0.0 -0.020 1.2347 ! !ions! CLA 0.0 -0.150 2.27 ! chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol HCL 0.0 -0.100 0.2245 !H+ proton, taken from Dan's files, under the name HCQ! *EDITED BY EFRAT* CE 0.000000 -0.068000 2.090000 !!For GPP!! HE1 0.000000 -0.031000 1.250000 ! ! for propene, yin/adm jr., 12/95 HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8 CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! propane pure solvent properties, adm jr, 2/3/92 CE1 0.000000 -0.068000 2.090000 ! ! for propene, yin/adm jr., 12/95 CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 ! ON2 0.0 -0.1521 1.77 !!for GOAc -patching the "acetylated N-terminus" (top_all36_prot.rtf) and GPP!! using par_all36_lipid.prm !par_all36_lipid.prm, CL=CD, OBL=OB, OSL=OS=ON2, CTL2=CT2=CN8, HAL=HA=HN8 CD 0.0 -0.0700 2.00 ! methyl acetate update OB 0.0 -0.12 1.70 0.0 -0.12 1.4 !FOR LOAc! CE2 0.000000 -0.064000 2.080000 ! ! for ethene, yin/adm jr., 12/95 HE2 0.000000 -0.026000 1.260000 ! ! for ethene, yin/adm jr., 12/95 HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp END File: loac.rtf ============== 27 1 RESI GPP -3 !! GROUP ATOM C2 CE1 -0.23 ATOM H21 HE1 0.12 ATOM C3 CN8 0.11 GROUP ATOM C4 CT2 -0.18 ATOM H41 HA 0.09 ATOM H42 HA 0.09 GROUP ATOM C5 CT2 -0.18 ATOM H51 HA 0.09 ATOM H52 HA 0.09 GROUP ATOM C6 CE1 -0.33 ATOM H61 HE1 0.22 ATOM C7 CE 0.11 GROUP ATOM C8 CT3 -0.27 ATOM H81 HA 0.09 ATOM H82 HA 0.09 ATOM H83 HA 0.09 GROUP ATOM C9 CT3 -0.27 ATOM H91 HA 0.09 ATOM H92 HA 0.09 ATOM H93 HA 0.09 GROUP ATOM C10 CT3 -0.27 ATOM H101 HA 0.09 ATOM H102 HA 0.09 ATOM H103 HA 0.09 GROUP ATOM C1 CE2 -0.10 ATOM H11 HE2 0.05 ATOM H12 HE2 0.05 GROUP ATOM O11 ON2 -0.52 !-0.62 ATOM P1 P 1.5 ATOM O2 ON3 -0.82 ATOM O3 ON3 -0.82 ATOM O4 ON2 -0.74 ATOM P2 P2 1.1 ATOM O5 ON3 -0.9 ATOM O6 ON3 -0.9 ATOM O7 ON3 -0.9 BOND C1 O11 C1 C2 C2 H21 BOND C1 H11 C1 H12 BOND C3 C4 C4 H41 C4 H42 BOND C4 C5 C5 H51 C5 H52 C5 C6 BOND C6 H61 C7 C8 C8 H81 C8 H82 BOND C8 H83 C7 C9 C9 H91 C9 H92 BOND C9 H93 BOND C3 C10 C10 H101 C10 H102 C10 H103 BOND O11 P1 P1 O2 P1 O3 P1 O4 BOND P2 O4 P2 O5 P2 O6 P2 O7 DOUBLE C1 C2 C6 C7 PRES ACEL 0.00 ! acetylated N-terminus (top_all36_prot.rtf) ! modified to match the LOAc -> turning GPP into LOAc! (by Efrat) GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY CD 0.52 ! CY=OY ATOM OY OB -0.26 ! | ATOM O1 ON2 -0.26 ! O1 DELETE ATOM O11 DELETE ATOM P1 DELETE ATOM O2 DELETE ATOM O3 DELETE ATOM O4 DELETE ATOM P2 DELETE ATOM O5 DELETE ATOM O6 DELETE ATOM O7 BOND O1 C3 BOND C2 C3 BOND CY CAY CY O1 CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY O1 OY ACCEPTOR OY CY IC CY O1 C1 C2 0.0000 0.0000 -60.0000 0.0000 0.0000 !IC CY C1 *O1 HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY O1 C1 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 RESI CLA -1.00 ! Chloride Ion GROUP ATOM CLA CLA -1.00 PATCHING FIRST NONE LAST NONE RESI HCL 1.00 ! Proton, positive hydrogen GROUP ATOM HCL HCL 1.00 PATCHING FIRST NONE LAST NONE END File: noeqchem.str ================== ! Add NOE restraints noe ! H-bonding interactions between the capsule's residues/monomers and the water molecules assign select atom RSRB 2 OH1 end select atom CWAT 6 OH2 end - kmin 0.0 rmin 2.78 kmax 250.0 rmax 2.84 fmax 500.0 assign select atom RSRB 4 OH1 end select atom CWAT 8 OH2 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom RSRD 2 OH1 end select atom CWAT 4 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRD 4 OH1 end select atom CWAT 2 OH2 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom RSRE 1 OH1 end select atom CWAT 4 OH2 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRE 2 OH1 end select atom CWAT 3 OH2 end - kmin 0.0 rmin 2.66 kmax 250.0 rmax 2.70 fmax 500.0 assign select atom RSRE 3 OH1 end select atom CWAT 6 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRE 4 OH1 end select atom CWAT 7 OH2 end - kmin 0.0 rmin 2.66 kmax 250.0 rmax 2.70 fmax 500.0 assign select atom RSRF 1 OH1 end select atom CWAT 2 OH2 end - kmin 0.0 rmin 2.71 kmax 250.0 rmax 2.75 fmax 500.0 assign select atom RSRF 2 OH1 end select atom CWAT 1 OH2 end - kmin 0.0 rmin 2.66 kmax 250.0 rmax 2.70 fmax 500.0 assign select atom RSRF 3 OH1 end select atom CWAT 8 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRF 4 OH1 end select atom CWAT 5 OH2 end - kmin 0.0 rmin 2.65 kmax 250.0 rmax 2.69 fmax 500.0 assign select atom CWAT 1 OH2 end select atom RSRC 1 OH1 end - kmin 0.0 rmin 2.80 kmax 250.0 rmax 2.84 fmax 500.0 assign select atom CWAT 1 OH2 end select atom RSRD 3 OH1 end - kmin 0.0 rmin 2.78 kmax 250.0 rmax 2.82 fmax 500.0 assign select atom CWAT 2 H1 end select atom RSRA 2 OH1 end - kmin 0.0 rmin 1.85 kmax 250.0 rmax 1.89 fmax 500.0 assign select atom CWAT 3 OH2 end select atom RSRA 1 OH1 end - kmin 0.0 rmin 2.79 kmax 250.0 rmax 2.85 fmax 500.0 assign select atom CWAT 3 OH2 end select atom RSRD 1 OH1 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom CWAT 4 OH2 end select atom RSRC 2 OH1 end - kmin 0.0 rmin 2.74 kmax 250.0 rmax 2.78 fmax 500.0 assign select atom CWAT 5 OH2 end select atom RSRB 3 OH1 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom CWAT 5 OH2 end select atom RSRA 3 OH1 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom CWAT 6 H2 end select atom RSRA 4 OH1 end - kmin 0.0 rmin 1.84 kmax 250.0 rmax 1.88 fmax 500.0 assign select atom CWAT 7 OH2 end select atom RSRB 1 OH1 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom CWAT 7 OH2 end select atom RSRC 3 OH1 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom CWAT 8 OH2 end select atom RSRC 4 OH1 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRA 1 OH1 end select atom RSRA 2 OH2 end - kmin 0.0 rmin 2.79 kmax 250.0 rmax 2.83 fmax 500.0 assign select atom RSRA 1 OH2 end select atom RSRE 3 OH2 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRA 2 OH1 end select atom RSRA 3 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRA 2 OH2 end select atom RSRD 1 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRA 3 OH1 end select atom RSRA 4 OH2 end - kmin 0.0 rmin 2.77 kmax 250.0 rmax 2.81 fmax 500.0 assign select atom RSRA 3 OH2 end select atom RSRF 1 OH2 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRA 4 OH1 end select atom RSRA 1 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRA 4 OH2 end select atom RSRB 3 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRB 1 OH1 end select atom RSRB 2 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRB 1 OH2 end select atom RSRB 4 OH1 end - kmin 0.0 rmin 2.78 kmax 250.0 rmax 2.82 fmax 500.0 assign select atom RSRB 2 OH2 end select atom RSRE 4 OH2 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRB 3 OH1 end select atom RSRB 4 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRB 3 OH2 end select atom RSRB 2 OH1 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRB 4 OH2 end select atom RSRF 4 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRC 1 OH1 end select atom RSRC 2 OH2 end - kmin 0.0 rmin 2.78 kmax 250.0 rmax 2.82 fmax 500.0 assign select atom RSRC 1 OH2 end select atom RSRF 3 OH2 end - kmin 0.0 rmin 2.74 kmax 250.0 rmax 2.78 fmax 500.0 assign select atom RSRC 2 OH1 end select atom RSRC 3 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRC 2 OH2 end select atom RSRD 3 OH2 end - kmin 0.0 rmin 2.74 kmax 250.0 rmax 2.78 fmax 500.0 assign select atom RSRC 3 OH1 end select atom RSRC 4 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRC 3 OH2 end select atom RSRE 1 OH2 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRC 4 OH1 end select atom RSRC 1 OH2 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRC 4 OH2 end select atom RSRB 1 OH2 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRD 1 OH1 end select atom RSRD 2 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRD 1 OH2 end select atom RSRD 4 OH1 end - kmin 0.0 rmin 2.78 kmax 250.0 rmax 2.82 fmax 500.0 assign select atom RSRD 2 OH2 end select atom RSRE 2 OH2 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRD 3 OH1 end select atom RSRD 4 OH2 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRD 3 OH2 end select atom RSRD 2 OH1 end - kmin 0.0 rmin 2.76 kmax 250.0 rmax 2.80 fmax 500.0 assign select atom RSRD 4 OH2 end select atom RSRF 2 OH2 end - kmin 0.0 rmin 2.74 kmax 250.0 rmax 2.78 fmax 500.0 assign select atom RSRE 1 OH2 end select atom RSRE 4 OH1 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRE 2 OH2 end select atom RSRE 1 OH1 end - kmin 0.0 rmin 2.74 kmax 250.0 rmax 2.78 fmax 500.0 assign select atom RSRE 3 OH2 end select atom RSRE 2 OH1 end - kmin 0.0 rmin 2.71 kmax 250.0 rmax 2.75 fmax 500.0 assign select atom RSRE 4 OH2 end select atom RSRE 3 OH1 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRF 1 OH2 end select atom RSRF 4 OH1 end - kmin 0.0 rmin 2.72 kmax 250.0 rmax 2.76 fmax 500.0 assign select atom RSRF 2 OH2 end select atom RSRF 1 OH1 end - kmin 0.0 rmin 2.75 kmax 250.0 rmax 2.79 fmax 500.0 assign select atom RSRF 3 OH2 end select atom RSRF 2 OH1 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 assign select atom RSRF 4 OH2 end select atom RSRF 3 OH1 end - kmin 0.0 rmin 2.73 kmax 250.0 rmax 2.77 fmax 500.0 end