s file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to dava@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; ;#include "trappeua.ff/forcefield.itp" #define trappeua [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ 1 1 no [ atomtypes ] ; _O indicates the (pseduo)atom is bonded to an oxygen. _C indicates the ; (pseudo)atom is bonded to a carbon. ; name bond_type mass charge ptype C6 Clam CH3_C CH3 15.03450 0.000 A 0.00819752345327 2.33014239486e-06; [CH3]-CHX CH2_C CH2 14.02660 0.000 A 0.00631986287433 4.48496002146e-06; (CHX)2-[CH2] CH_C CH 13.01900 0.000 A 0.002764768497 3.64762596488e-06; (CHX)3-[CH] C_C C 12.01100 0.000 A 0.002764768497 3.64762596488e-06; (CHX)4-[C] [ nonbond_params ] ; i j func C6 Clam CH3_C CH2_C 1 0.00726864063375 3.3075463302e-06; cross-interactions for CH3_C and CH2_C CH3_C CH_C 1 0.00489378022934 3.10910301117e-06; cross-interactions for CH3_C and CH_C CH3_C C_C 1 0.00489378022934 3.10910301117e-06; cross-interactions for CH3_C and C_C CH2_C CH_C 1 0.00419893969751 4.08742151221e-06; cross-interactions for CH2_C and CH_C CH2_C C_C 1 0.00419893969751 4.08742151221e-06; cross-interactions for CH2_C and C_C CH_C C_C 1 0.00419893969751 4.08742151221e-06; cross-interactions for CH_C and C_C [ bondtypes ] ; i j func b0 k0 ; CHX-CHY CH3 CH3 1 0.1540 502416.0 CH3 CH2 1 0.174 502416.0 CH3 CH 1 0.174 502416.0 CH3 C 1 0.174 502416.0 CH2 CH 1 0.1540 502416.0 CH2 C 1 0.1540 502416.0 CH C 1 0.1540 502416.0 [ angletypes ] ; i j k func th0 cth ; CHX-[CH2]-CHY CH3 CH2 CH3 1 114.0 519.65389 CH3 CH2 CH2 1 114.0 519.65389 CH3 CH2 CH 1 114.0 519.65389 CH3 CH2 C 1 114.0 519.65389 CH2 CH2 CH2 1 114.0 519.65389 CH2 CH2 CH 1 114.0 519.65389 CH2 CH2 C 1 114.0 519.65389 CH CH2 CH 1 114.0 519.65389 CH CH2 C 1 114.0 519.65389 C CH2 C 1 114.0 519.65389 ; CHX-[CH]-CHY CH3 CH CH3 1 112.0 519.65389 CH3 CH CH2 1 112.0 519.65389 CH3 CH CH 1 112.0 519.65389 CH3 CH C 1 112.0 519.65389 CH2 CH CH2 1 112.0 519.65389 CH2 CH CH 1 112.0 519.65389 CH2 CH C 1 112.0 519.65389 CH CH CH 1 112.0 519.65389 CH CH C 1 112.0 519.65389 C CH C 1 112.0 519.65389 ; CHX-[C]-CHY CH3 C CH3 1 109.47 519.65389 CH3 C CH2 1 109.47 519.65389 CH3 C CH 1 109.47 519.65389 CH3 C C 1 109.47 519.65389 CH2 C CH2 1 109.47 519.65389 CH2 C CH 1 109.47 519.65389 CH2 C C 1 109.47 519.65389 CH C CH 1 109.47 519.65389 CH C C 1 109.47 519.65389 C C C 1 109.47 519.65389 [ dihedraltypes ] ; Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans using the ; following formulas, where F indicates values from Table 1 of Chen or Table 2 ; of Martin. ; C0 = F0 + F1 + 2F2 + F3 ; C1 = -F1 + 3F3 ; C2 = -2F2 + 8F4 ; C3 = -4F3 ; C4 = -8F4 ; C5 = 0 ; i j k l func C0 C1 C2 C3 C4 C5 ; CHX-[CH2]-[CH2]-CHY CH3 CH2 CH2 CH3 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH3 CH2 CH2 CH2 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH3 CH2 CH2 CH 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH3 CH2 CH2 C 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH2 CH2 CH2 CH2 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH2 CH2 CH2 CH 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH2 CH2 CH2 C 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH CH2 CH2 CH 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 CH CH2 CH2 C 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 C CH2 CH2 C 3 8.39736 16.78632 1.13393 -26.31760 0.00000 0.00000 ; CHX-[CH2]-[CH]-CHY CH3 CH2 CH CH3 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH2 CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH2 CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH2 CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH2 CH CH3 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH2 CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH2 CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH2 CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH2 CH CH3 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH2 CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH2 CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH2 CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 C CH2 CH CH3 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 C CH2 CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 C CH2 CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 C CH2 CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 ; CHX-[CH2]-[C]-CHY CH3 CH2 C CH3 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH3 CH2 C CH2 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH3 CH2 C CH 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH3 CH2 C C 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH2 CH2 C CH3 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH2 CH2 C CH2 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH2 CH2 C CH 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH2 CH2 C C 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH CH2 C CH3 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH CH2 C CH2 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH CH2 C CH 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 CH CH2 C C 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 C CH2 C CH3 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 C CH2 C CH2 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 C CH2 C CH 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 C CH2 C C 3 3.83538 11.50613 0.00000 -15.34151 0.00000 0.00000 ; CHX-[CH]-[CH]-CHY CH3 CH CH CH3 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH3 CH CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH CH CH2 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH2 CH CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH CH CH 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 CH CH CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 C CH CH C 3 3.28629 7.44211 1.85995 -14.67569 0.00000 0.00000 [ moleculetype ] ; Name nrexcl IC4H10 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3_C 1 IC4H10 CAA 1 0.000 15.0345 2 CH_C 1 IC4H10 CAB 2 0.000 13.01900 3 CH3_C 1 IC4H10 CAC 3 0.000 15.0345 4 CH3_C 1 IC4H10 CAD 4 0.000 15.0345 [ bonds ] ; ai aj 1 2 1 0.174 502416.0; CAA CAB 2 3 1 0.174 502416.0; CAC CAD 2 4 1 0.174 502416.0; CAA CAB [ angles ] ; ai aj ak 1 2 3 1 112.0 519.65389; CAA CAB CAC 1 2 4 1 112.0 519.65389; CAB CAC CAD 3 2 4 1 112.0 519.65389; CAB CAC CAD [ dihedrals ] ; ai aj ak al [ system ] IC4H10 box [ molecules ] IC4H10 400