Please make sure that the error exists in the latest version. Either 4.5.1 or if you know how please check the latest GIT version from release-4-5-patches. If you still get the error with the latest version, please file a bugzilla report and attach all required files.
On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep <m.alif.m.la...@gmail.com>wrote: > Dear Gromacs Users and Developers, > > I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic > liquid MD simulation using amber 99 force field. I got my topology from > topolbuild v 1.3. I successfully minimized both cation and anion separately > using cg and steep. Then I include the anion in the cation system using > genbox. I got error from grompp like this: > > ------------------------------------------------------------------------------ > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# > checking input for internal consistency... > processing topology... > Generated 2211 of the 2211 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 2211 of the 2211 1-4 parameter combinations > Segmentation fault (core dumped) > [a...@neox MD1]$ > > --------------------------------------------------------------------------------- > Still cant find my answer in the mailing list. Sorry for the large post, > but here's my .mdp and .top > > > --------------------------------------------------------------------------------- > title = Conjugated-Gradients Energy Minimization > > ; Preprocessing > cpp = /lib/cpp > include = -I../top > > ; Parameters > integrator = cg > emtol = 1.0 > nsteps = 5000 > nstenergy = 100 > nstxtcout = 100 > xtc_grps = System > energygrps = System > > ; Neighboursearching > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 0.9 > constraints = none > pbc = xyz > > ----------------------------------------------------------------------------------------------------- > ; Topology from .mol2 file > ; topolbuild version 1.3 > ; Command line: > ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME > ; > ; The force field files to be included > #include "amber99.ff/forcefield.itp" > > [ moleculetype ] > ; name nrexcl > BMIM 3 > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 CT 1 BMIM C 1 -0.17243 12.01100 ; > -0.1724300 > 2 HC 1 BMIM H 1 0.07139 1.00800 ; > -0.1010400 > 3 HC 1 BMIM H 1 0.05434 1.00800 ; > -0.0467000 > 4 HC 1 BMIM H 1 0.05138 1.00800 ; > 0.0046800 > 5 CT 1 BMIM C 2 0.02353 12.01100 ; > 0.0282100 > 6 HC 1 BMIM H 2 0.02417 1.00800 ; > 0.0523800 > 7 HC 1 BMIM H 2 0.02427 1.00800 ; > 0.0766500 > 8 CT 1 BMIM C 3 0.01014 12.01100 ; > 0.0867900 > 9 HC 1 BMIM H 3 0.03312 1.00800 ; > 0.1199100 > 10 HC 1 BMIM H 3 0.02952 1.00800 ; > 0.1494300 > 11 NA 1 BMIM N 4 0.05435 14.00670 ; > 0.2037800 > 12 CC 1 BMIM C 4 -0.17380 12.01100 ; > 0.0299800 > 13 H4 1 BMIM H 4 0.23709 1.00800 ; > 0.2670700 > 14 NA 1 BMIM N 6 0.07275 14.00670 ; > 0.3398200 > 15 CT 1 BMIM C 5 -0.07367 12.01100 ; > 0.2661500 > 16 H1 1 BMIM H 5 0.10657 1.00800 ; > 0.3727200 > 17 H1 1 BMIM H 5 0.09108 1.00800 ; > 0.4638000 > 18 CC 1 BMIM C 6 -0.08433 12.01100 ; > 0.3794700 > 19 H4 1 BMIM H 6 0.20500 1.00800 ; > 0.5844700 > 20 CR 1 BMIM C 7 -0.02624 12.01100 ; > 0.5582300 > 21 H5 1 BMIM H 7 0.21862 1.00800 ; > 0.7768500 > 22 CT 1 BMIM C 8 -0.18403 12.01100 ; > 0.5928200 > 23 H1 1 BMIM H 8 0.13823 1.00800 ; > 0.7310500 > 24 H1 1 BMIM H 8 0.13886 1.00800 ; > 0.8699100 > 25 H1 1 BMIM H 8 0.13010 1.00800 ; > 1.0000100 > ; total molecule charge = 1.0000100 > > [ bonds ] > ; ai aj funct b0 kb > 1 5 1 0.15260 259408. ; C- C > 1 2 1 0.10900 284512. ; C- H > 1 3 1 0.10900 284512. ; C- H > 1 4 1 0.10900 284512. ; C- H > 5 8 1 0.15260 259408. ; C- C > 5 6 1 0.10900 284511. ; C- H > 5 7 1 0.10900 284512. ; C- H > 8 15 1 0.15260 259408. ; C- C > 8 9 1 0.10900 284512. ; C- H > 8 10 1 0.10900 284512. ; C- H > 11 12 1 0.13850 353129. ; N- C > 11 15 1 0.13850 353129. ; N- C > 11 20 1 0.13850 353129. ; N- C > 12 18 1 0.14000 392459. ; C- C > 12 13 1 0.10800 307106. ; C- H > 14 18 1 0.13850 353129. ; N- C > 14 20 1 0.13850 353129. ; N- C > 14 22 1 0.13850 353129. ; N- C > 15 16 1 0.10900 284512. ; C- H > 15 17 1 0.10900 284512. ; C- H > 18 19 1 0.10800 307106. ; C- H > 20 21 1 0.10800 307106. ; C- H > 22 23 1 0.10900 284512. ; C- H > 22 24 1 0.10900 284512. ; C- H > 22 25 1 0.10900 284512. ; C- H > > [ pairs ] > 2 8 1 ; H- C > 2 6 1 ; H- H > 2 7 1 ; H- H > 3 8 1 ; H- C > 3 6 1 ; H- H > 3 7 1 ; H- H > 4 8 1 ; H- C > 4 6 1 ; H- H > 4 7 1 ; H- H > 1 15 1 ; C- C > 1 9 1 ; C- H > 1 10 1 ; C- H > 6 15 1 ; H- C > 6 9 1 ; H- H > 6 10 1 ; H- H > 7 15 1 ; H- C > 7 9 1 ; H- H > 7 10 1 ; H- H > 5 11 1 ; C- N > 5 16 1 ; C- H > 5 17 1 ; C- H > 9 11 1 ; H- N > 9 16 1 ; H- H > 9 17 1 ; H- H > 10 11 1 ; H- N > 10 16 1 ; H- H > 10 17 1 ; H- H > 15 18 1 ; C- C > 15 13 1 ; C- H > 20 13 1 ; C- H > 12 8 1 ; C- C > 12 16 1 ; C- H > 12 17 1 ; C- H > 20 8 1 ; C- C > 20 16 1 ; C- H > 20 17 1 ; C- H > 12 21 1 ; C- H > 15 14 1 ; C- N > 15 21 1 ; C- H > 11 19 1 ; N- H > 13 14 1 ; H- N > 13 19 1 ; H- H > 20 19 1 ; C- H > 22 12 1 ; C- C > 22 19 1 ; C- H > 18 21 1 ; C- H > 22 11 1 ; C- N > 22 21 1 ; C- H > 18 23 1 ; C- H > 18 24 1 ; C- H > 18 25 1 ; C- H > 20 23 1 ; C- H > 20 24 1 ; C- H > 20 25 1 ; C- H > > [ angles ] > ; ai aj ak funct th0 cth > 2 1 5 1 109.500 418.4000 ; H- C- C > 3 1 5 1 109.500 418.4000 ; H- C- C > 4 1 5 1 109.500 418.4000 ; H- C- C > 1 5 8 1 109.500 334.7200 ; C- C- C > 1 5 6 1 109.500 418.4000 ; C- C- H > 1 5 7 1 109.500 418.4000 ; C- C- H > 3 1 2 1 109.500 292.8800 ; H- C- H > 4 1 2 1 109.500 292.8800 ; H- C- H > 4 1 3 1 109.500 292.8800 ; H- C- H > 6 5 8 1 109.500 418.4000 ; H- C- C > 7 5 8 1 109.500 418.4000 ; H- C- C > 5 8 15 1 109.500 334.7200 ; C- C- C > 5 8 9 1 109.500 418.4000 ; C- C- H > 5 8 10 1 109.500 418.4000 ; C- C- H > 7 5 6 1 109.500 292.8800 ; H- C- H > 9 8 15 1 109.500 418.4000 ; H- C- C > 10 8 15 1 109.500 418.4000 ; H- C- C > 8 15 11 1 109.500 418.4000 ; C- C- N > 8 15 16 1 109.500 418.4000 ; C- C- H > 8 15 17 1 109.500 418.4000 ; C- C- H > 10 8 9 1 109.500 292.8800 ; H- C- H > 15 11 12 1 126.400 585.7600 ; C- N- C > 20 11 12 1 120.000 585.7600 ; C- N- C > 11 12 18 1 126.400 585.7600 ; N- C- C > 11 12 13 1 120.000 418.4000 ; N- C- H > 20 11 15 1 126.400 585.7600 ; C- N- C > 11 15 16 1 109.500 418.4000 ; N- C- H > 11 15 17 1 109.500 418.4000 ; N- C- H > 11 20 14 1 120.000 585.7600 ; N- C- N > 11 20 21 1 120.000 418.4000 ; N- C- H > 13 12 18 1 120.000 418.4000 ; H- C- C > 12 18 14 1 126.400 585.7600 ; C- C- N > 12 18 19 1 120.000 418.4000 ; C- C- H > 20 14 18 1 120.000 585.7600 ; C- N- C > 22 14 18 1 126.400 585.7600 ; C- N- C > 14 18 19 1 120.000 418.4000 ; N- C- H > 22 14 20 1 120.000 585.7600 ; C- N- C > 14 20 21 1 120.000 418.4000 ; N- C- H > 14 22 23 1 109.500 418.4000 ; N- C- H > 14 22 24 1 109.500 418.4000 ; N- C- H > 14 22 25 1 109.500 418.4000 ; N- C- H > 17 15 16 1 109.500 292.8800 ; H- C- H > 24 22 23 1 109.500 292.8800 ; H- C- H > 25 22 23 1 109.500 292.8800 ; H- C- H > 25 22 24 1 109.500 292.8800 ; H- C- H > > [ dihedrals ] > ; ai aj ak al funct phi0 cp mult > 2 1 5 8 1 0.000 0.669 3 ; dih > H- C- C- C > 1 5 8 15 1 0.000 0.753 3 ; dih > C- C- C- C > 1 5 8 15 1 180.000 1.046 2 ; dih > C- C- C- C > 1 5 8 15 1 180.000 0.837 1 ; dih > C- C- C- C > 5 8 15 11 1 0.000 0.651 3 ; dih > C- C- C- N > 20 11 12 18 9 180.0 5.85760 2 ; dih > C- N- C- C > 12 11 15 8 1 0.000 0.000 2 ; dih > C- N- C- C > 12 11 20 14 9 180.0 5.85760 2 ; dih > C- N- C- N > 11 12 18 14 1 180.000 15.167 2 ; dih > N- C- C- N > 20 14 18 12 9 180.0 5.85760 2 ; dih > C- N- C- C > 18 14 20 11 9 180.0 5.85760 2 ; dih > C- N- C- N > 18 14 22 23 1 0.000 0.000 2 ; dih > C- N- C- H > 11 12 15 20 1 180.000 4.602 2 ; imp > N- C- C- C > 12 11 18 13 1 180.000 4.602 2 ; imp > C- N- C- H > 14 18 20 22 1 180.000 4.602 2 ; imp > N- C- C- C > 18 12 14 19 1 180.000 4.602 2 ; imp > C- C- N- H > 20 11 14 21 1 180.000 4.602 2 ; imp > C- N- N- H > > ; Include Position restraint file > ; WARNING: Position restraints and distance restraints ought not be done > together > #ifdef POSRES > #include "posreBMIM_Test3.itp" > #endif > > ; Include TFO topology > #include TFO_amber99.itp > > ; Include water topology > #include "tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include generic topology for ions > #include "ions.itp" > > [ system ] > ; title from mol2 input > BMIMTFO > > [ molecules ] > ; molecule name nr. > BMIM 1 > TFO 1 > > -------------------------------------------------------------------------------------------- > Any thought, advice and support is greatly appreciated. Thank you. > > -Alif- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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