Dear Justin and All Right now, I am trying to add new residue in OPLS-aa ff when I make the following grompp -f file.mdp -c file.gro -p file.top -o file I have the following error > -------------------- > Program grompp, VERSION 4.5.2 > Source code file: toppush.c, line: 1071 > > Fatal error: > Atoms in the .top are not numbered consecutively from 1 (rather, > atomnr = -89390831, while at->nr = 0) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors- > ---------------- These are my files 0- file forcefiel.itp [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 1- file.rtp ; Ion thiocyanate adiciionado [ SCN ] [ atoms ] SQ opls_966 -0.750 1 CQ opls_967 0.490 1 NQ opls_968 -0.740 1 [ bonds ] CQ SQ CQ NQ 2- file.atp opls_966 32.06000 ; SQ (SCN-) opls_967 12.01100 ; CQ (SCN-) opls_968 14.00670 ; NQ (SCN-) 3- file ffbonded.itp [ bondtypes ] ; i j func b0 kb CQ SQ 1 0.16700 284082.0 ; JChemPhys_2008_118_154504 CQ NQ 1 0.11900 122389e1 ; JChemPhys_2008_118_154504 [ angletypes ] ; i j k func th0 cth SQ CQ NQ 1 180.000 652.802 ;JChemPhys_2008_118_154504 4- file ffnonbonded.itp [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_type mass charge ptype sigma epsilon opls_966 SQ 16 32.06000 -0.750 A 3.55000e-01 1.04600e+00 opls_967 CQ 6 12.01100 0.490 A 3.75000e-01 4.39320e-01 opls_968 NQ 7 14.00670 -0.740 A 3.25000e-01 7.11280e-01 5. file minimization.mdp ; Minimization integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 dt = 0.01 ns_type = grid pbc = xyz ;Electrostatic coulombtype = PME pme_order = 4 fourierspacing = 0.12 rcoulomb = 0.9 rvdw = 0.9 6. file .gro SCN THIOCYANATE ION 3 1SCN SQ 1 1.720 1.647 1.785 1SCN CQ 2 1.640 1.651 1.631 1SCN NQ 3 1.590 1.653 1.534 3.30000 3.30000 3.30000 7 file.top [ moleculetype ] ; Name nrexcl Ion 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB ch argeB massB ; residue 1 SCN rtp SCN q -1.0 1 opls_966 1 SCN SQ 1 -0.75 32.06 ; qtot -0. 75 2 opls_967 1 SCN CQ 1 0.49 12.011 ; qtot -0. 26 3 opls_968 1 SCN NQ 1 -0.74 14.0067 ; qtot -1 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 2 3 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 ; Include topology for ions #include "./modif.ff/ions.itp" [ system ] ; Name SCN THIOCYANATE ION [ molecules ] ; Compound #mols Ion 1 Thanks, Ana GomezStudent
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