[gmx-users] Grompp Error : Segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 28 18:23:07 CEST 2010
Roland Schulz wrote:
> 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.
>
My first guess would be that these lines are problematic:
; Include TFO topology
#include TFO_amber99.itp
The .itp filename should be enclosed in quotes.
-Justin
> On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep <m.alif.m.latif at gmail.com
> <mailto:m.alif.m.latif at 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)
> [alif at 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-
>
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>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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