On 5/7/12 7:41 AM, Sarath Kumar Baskaran wrote:
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....
PRODRG produces (poor quality) topologies for Gromos96 43A1, not Gromos87 (or
"ffgmx"). One should not use ffgmx for new simulations as it does not perform
as well as newer force fields (and other reasons described in the 4.5 manual.
Using 43A1 will solve this particular problem, but do note that the PRODRG
topology will almost invariably require manual improvements.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
-Justin
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.*
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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