On 11/12/13 10:07 AM, Atila Petrosian wrote:
Dear all
My system contains protein + cnt + water molecules.
I have summarized what I did below:
-----------------------------------------------------------------------------------
1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then
I converted it into pr.itp by deleting
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
from begining of file and by deleting
; Include water topology
#include "charmm27.ff/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 topology for ions
#include "charmm27.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
from ending of file.
------------------------------------------------------------------------------------
2) I used bonded and nonbonded parameters for cnt from paper:
J. Phys. Chem. B 2001, 105, 9980-9987
(Carbon Nanotubes in Water: Structural Characteristics and Energetics).
I created cnt.ff folder containing following files:
ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp /
forcefield.itp
Then, I put cnt.ff folder in GMXLIB directory.
------------------------------------------------------------------------------------
3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for
cnt then I converted it into cnt.itp by deleting
; Include forcefield parameters
#include "cnt.ff/forcefield.itp"
from begining of file and by deleting
[ system ]
; Name
CNT
[ molecules ]
; Compound #mols
CNT 1
from ending of file.
------------------------------------------------------------------------------------
4) I combined cnt and protein to create one coordination file (system.gro).
Order of molecules are as follows: 1) cnt 2) protein
3) water.
------------------------------------------------------------------------------------
5) I wrote a topol.top file given below,
; Include forcefield parameters
#include "cnt.ff/forcefield.itp"
#include "cnt.itp"
#include "charmm27.ff/forcefield.itp"
#include "pr.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "charmm27.ff/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 topology for ions
#include "charmm27.ff/ions.itp"
[ system ]
; Name
CNT/Protein/SOL
[ molecules ]
; Compound #mols
CNT 1
Protein 1
SOL 1359
------------------------------------------------------------------------------------
When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I
encountered with following error:
Fatal error:
Syntax error - File forcefield.itp, line 11
Last line read:
'[ defaults ]'
Invalid order for directive defaults
Content of forcefield.itp in cnt.ff directory is as follows:
*******************************************************************************
* CHARMM port writted
by *
* Par Bjelkmar, Per Larsson, Michel
Cuendet, *
* Berk Hess and Erik
Lindahl. *
*
Correspondance: *
* bjelk...@cbr.su.se or lind...@cbr.su.se
*
*******************************************************************************
#define _FF_CNT
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
#include "ffcntnonbon.itp"
#include "ffcntbon.itp"
and
Content of forcefield.itp in Charmm27.ff directory is as follows:
*******************************************************************************
* CHARMM port writted
by *
* Par Bjelkmar, Per Larsson, Michel
Cuendet, *
* Berk Hess and Erik
Lindahl. *
*
Correspondance: *
* bjelk...@cbr.su.se or lind...@cbr.su.se
*
*******************************************************************************
#define _FF_CHARMM
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
#include "ffnanonbonded.itp"
#include "ffnabonded.itp"
------------------------------------------------------------------------------------
In both of forcefield.itp files, line 11 is [ defaults ].
I changed name of forcefield.itp file in cnt.ff directory to cntff.itp,
but there is same error, again.
That is all what I exactly did. Is anything wrong or missing?
How to solve this error?
You've already stated exactly what the problem is - you have two files that have
a [defaults] directive. You can't do that. You can only define this directive
once in a topology.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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