; ; File '6lyz_gmx.top' was generated ; By user: sunhwan (40816) ; On host: kuta ; At date: Fri Nov 10 13:02:26 2017 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2017-dev-20170822-762c6f0 (-: ; ; Executable: /home/sunhwan/local/gromacs/src/gromacs/build/bin/gmx ; Data prefix: /home/sunhwan/local/gromacs/src/gromacs (source tree) ; Working dir: /data/sunhwan/work/lysozyme/1_setup ; Command line: ; gmx pdb2gmx -f 6lyz_4pdb2gmx.pdb -o 6lyz_gmx.pdb -p 6lyz_gmx.top -ff charmm36 -water tip3p -ter -merge all ; Force field was read from current directory or a relative path - path added. ; [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 [ atomtypes ] ;type atnum mass charge ? sigma epsilon CG2R61 6 12.011000 0.000 A 0.355005321205 0.29288 HGR61 1 1.008000 0.000 A 0.242003727796 0.12552 LP 0 0.000000 0.00 A 0.0 0.0 ; pram ; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01 [ nonbond_params ] LP LP 1 1.069078461768 0.041840000000 ; pram [ bondtypes ] ; i j func b0 kb CG2R61 CG2R61 1 0.13750000 255224.00 CG2R61 HGR61 1 0.10800000 284512.00 [ angletypes ] ; i j k func theta0 ktheta ub0 kub CG2R61 CG2R61 CG2R61 5 120.000000 334.720000 0.24162000 29288.00 CG2R61 CG2R61 HGR61 5 120.000000 251.040000 0.21525000 18409.60 [ dihedraltypes ] ; i j k l func phi0 kphi mult CG2R61 CG2R61 CG2R61 CG2R61 9 180.000000 12.970400 2 CG2R61 CG2R61 CG2R61 HGR61 9 180.000000 17.572800 2 HGR61 CG2R61 CG2R61 HGR61 9 180.000000 10.041600 2 [ dihedraltypes ] ; 'improper' dihedrals ; i j k l func phi0 kphi [ moleculetype ] ; Name nrexcl BENX 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 BENX rtp BENX q 0.0 1 CG2R61 1 BENX CG 1 -0.115 12.011 ; qtot -0.115 2 HGR61 1 BENX HG 1 0.115 1.008 ; qtot 0 3 CG2R61 1 BENX CD1 1 -0.115 12.011 ; qtot -0.115 4 HGR61 1 BENX HD1 1 0.115 1.008 ; qtot 0 5 CG2R61 1 BENX CD2 1 -0.115 12.011 ; qtot -0.115 6 HGR61 1 BENX HD2 1 0.115 1.008 ; qtot 0 7 CG2R61 1 BENX CE1 1 -0.115 12.011 ; qtot -0.115 8 HGR61 1 BENX HE1 1 0.115 1.008 ; qtot 0 9 CG2R61 1 BENX CE2 1 -0.115 12.011 ; qtot -0.115 10 HGR61 1 BENX HE2 1 0.115 1.008 ; qtot 0 11 CG2R61 1 BENX CZ 1 -0.115 12.011 ; qtot -0.115 12 HGR61 1 BENX HZ 1 0.115 1.008 ; qtot 0 13 LP 1 BENX LPA 1 0.000 0.000 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 5 1 3 4 1 3 7 1 5 6 1 5 9 1 7 8 1 7 11 1 9 10 1 9 11 1 11 12 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 8 1 1 10 1 1 11 1 2 4 1 2 6 1 2 7 1 2 9 1 3 6 1 3 9 1 3 12 1 4 5 1 4 8 1 4 11 1 5 7 1 5 12 1 6 10 1 6 11 1 7 10 1 8 9 1 8 12 1 10 12 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 5 2 1 5 5 3 1 5 5 1 3 4 5 1 3 7 5 4 3 7 5 1 5 6 5 1 5 9 5 6 5 9 5 3 7 8 5 3 7 11 5 8 7 11 5 5 9 10 5 5 9 11 5 10 9 11 5 7 11 9 5 7 11 12 5 9 11 12 5 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 3 4 9 2 1 3 7 9 5 1 3 4 9 5 1 3 7 9 2 1 5 6 9 2 1 5 9 9 3 1 5 6 9 3 1 5 9 9 1 3 7 8 9 1 3 7 11 9 4 3 7 8 9 4 3 7 11 9 1 5 9 10 9 1 5 9 11 9 6 5 9 10 9 6 5 9 11 9 3 7 11 9 9 3 7 11 12 9 8 7 11 9 9 8 7 11 12 9 5 9 11 7 9 5 9 11 12 9 10 9 11 7 9 10 9 11 12 9 [ virtual_sites2 ] ; Vsite from funct a 13 1 11 1 0.500 [ system ] ; Name two benzene [ molecules ] ; Compound #mols BENX 2