[gmx-users] itp file problem

Sarath Kumar Baskaran bskumar.tech at gmail.com
Mon May 7 13:41:24 CEST 2012


First i had simulation of the protein alone in united atom gromacs force
field by -ff gmx in pdb2gmx
now i am unable to run the protein-ligand complex for the same protein with
a ligand,
 it says the following error due to itp file generated from PRODRG,
if i change the force field its says atom mismatch............. Please help
me....

What is the way to run the simulation

grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr
                         :-)  G  R  O  M  A  C  S  (-:

               GRoups of Organic Molecules in ACtion for Science

                            :-)  VERSION 4.0.7  (-:


      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-4.0.7  (-:

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  prt_b4ion.pdb  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p        prt.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o  prt_b4ion.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-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.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
processing
-[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

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp

-------------------------------------------------------
Program grompp-4.0.7, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype CR1 not found
-------------------------------------------------------

"I Caught It In the Face" (P.J. Harvey)

[

 grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr
                         :-)  G  R  O  M  A  C  S  (-:

                          GROtesk MACabre and Sinister

                            :-)  VERSION 4.0.7  (-:


      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-4.0.7  (-:

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  prt_b4ion.pdb  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p        prt.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o  prt_b4ion.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-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.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
processing
-[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

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp
Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'DRG'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file prt.top, line 18947]:
  System has non-zero total charge: -9.999978e-01



processing coordinates...

-------------------------------------------------------
Program grompp-4.0.7, VERSION 4.0.7
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (prt_b4ion.pdb, 79463)
             does not match topology (prt.top, 79455)
-------------------------------------------------------

"Sometimes Life is Obscene" (Black Crowes)


-- 
-- 

*Yours Sincerely,*
*B. Sarath Kumar, M.S (By Research),
Tissue Culture and Drug Discovery Lab,
Centre for Biotechnology,
Anna University, Chennai.*
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