Fwd: [gmx-users] add hydrogen atom in pdb file
nafiseh farhadian
na.farhadian at gmail.com
Tue Dec 16 21:19:27 CET 2008
Dear Sir,
thanks for your attention. i changed the force filed to ''ffgmx2'' and
''ffG43a1'' but i receive a new fatal error abou ''atom type''.
for the next suggestion i addes ''ffgmx.hdb'' to the topology file but there
was alot of error as you see. what shall i do?
This is my topology file
#define HEAVY_H
; Include forcefield parameters
#include "ffgmx.itp"
; Include hydrogen data bank
#include "ffgmx.hdb"
; Include protein topology
#include "top_A.itp"
; Include protein topology
#include "top_B.itp"
; Include ibuprofen topology
#include "ib.itp"
; Include water topology
#include "spc.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 ]
; Name
ibuprofen in HSA
[ molecules ]
; Compound #mols
Protein_A 3
Protein_B 0
Na 45
----------------------------------------------
this is my command in gromacs: grompp -f em.mdp -c ucell-box.pdb -p HSA.top
-o em.tpr
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c ucell-box.pdb Input Generic structure: gro g96 pdb tpr tpb tpa
xml
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-n index.ndx Input, Opt. Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p HSA.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o em.tpr Output Generic run input: tpr tpb tpa xml
-t traj.trr Input, Opt. Full precision trajectory: trr trj
-e ener.edr Input, Opt. Generic energy: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarn int 10 Number of warnings after which input processing
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waals
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
WARNING 1 [file em.mdp, line unknown]:
Unknown left-hand 'bd-temp' in parameter file
checking input for internal consistency...
calling /lib/cpp...
In file included from HSA.top:22:
top_B.itp:35345:9: warning: no newline at end of file
processing topology...
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 1]:
*Incorrect number of atomtypes* for dihedral (1 instead of 2 or 4)
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 2]:
Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 3]:
Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 4]:
Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
.
.
.
ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 146]:
Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
Generated 1284 of the 1485 non-bonded parameter combinations
WARNING 2 [file "top_B.itp", line 35345]:
Too few parameters on line (source file toppush.c, line 1168)
Excluding 3 bonded neighbours for Protein_A 3
Excluding 3 bonded neighbours for Protein_B 0
Excluding 1 bonded neighbours for Na 45
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469
*Fatal error:
number of coordinates in coordinate file (ucell-box.pdb, 18400)
does not match topology (HSA.top, 17574)
*-------------------------------------------------------
On Sun, Dec 14, 2008 at 11:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> nafiseh farhadian wrote:
>
>> Dear Sir,
>> i'm one of the new gmx user. i have a problem with gromacs input file.
>> i'll be thanking if you help me.
>> i'm working on protein system. i have pdb and itp file. in itp file there
>> are hydrogen atoms but in pdb file no. so when i define top file the number
>> of atoms don't match to each other and i get a fattal error. my forcefield
>> in top file is ''ffgmx forcefield''. i'll be appriciate if you help me.
>>
>
> Don't use ffgmx for new simulations... it's been deprecated for years, and
> pdb2gmx points this out.
>
> It's also always appropriate to cite the actual error message you received,
> since if your interpretation of the problem was totally reliable then you
> probably wouldn't need to be asking for help.
>
> You might try the protonate utility, or using pdb2gmx on your structure to
> generate your .top file.
>
> Mark
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