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.la...@gmail.com
<mailto: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-
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ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
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--
========================================
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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