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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
; 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
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                                :-)  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
  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
  -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
-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
-[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
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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