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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