[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Wed Aug 19 01:33:50 CEST 2009
Hi Justin,
I am using these commands...
genbox -cp 1K4C.pdb -box 10 10 10 -o 1K4C.gro
from here I can get my 1K4C.gro file.
As far as CG structure of protein is concerned I can produce the CG
structure using awk script like this..
awk -f atom2cg.awk 1K4C.pdb > 1K4C_CG.pdb
But after getting the CG structure its difficult to get the .itp file for
1K4C_CG.pdb because dssp does not produce .ssd files for CG structure of
proteins and if I am not having .ssd file then i cant get 1K4C_CG.itp file
so thats why I did not use awk script and I was just doing for the normal
protein to test first.
Here is the error------------
grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10
:-) G R O M A C S
(-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.0.5 (-:
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 1K4C.gro 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 1K4C.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.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 10 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'
Replacing old mdp entry 'unconstrained_start' by 'continuation'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
checking input for internal consistency...
NOTE 1 [file em.mdp, line unknown]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rcoulomb.
NOTE 2 [file em.mdp, line unknown]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
NOTE 3 [file 1K4C.top, line 15]:
System has non-zero total charge: 4.000000e+00
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (1K4C.gro, 4534)
does not match topology (1K4C.top, 1166)
On Tue, Aug 18, 2009 at 7:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> sunny mishra wrote:
>
>> Ok. Thanks but I am doing a small test to make the .top file and .gro
>> files of fresh 1K4C protein structure without removing anything but when I
>> run my grommp command to minimize it as I asked earlier as well it says
>> number of atoms in the .top are not equal to .top file and as you said that
>> without adding any other molecule I just have to fix the [molecules]
>> section, but it doesn't fix.
>>
>> here are some details of my .top file which I created on my own after
>> getting the 1K4C.itp file. I got 1K4C.itp file something like this..
>>
>> grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq)
>> dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp)
>> dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd)
>>
>> seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp
>>
>
> <snip>
>
> and after that I produce my 1K4C.gro file from genbox or editconf and then
>> when i run the command grommp it says that number of atoms in .gro
>>
>
> What commands are you giving genbox/editconf? You've never invoked the awk
> script that converts an atomistic protein structure to CG (provided by the
> MARTINI folks). Could that be the cause of the disconnect? Without seeing
> the actual error message, the best anyone can do is guess.
>
> -Justin
>
> file are unequal to .top file. Since I am doing the simulation in vacuum I
>> cannot add anything else. Don't know how to proceed.
>>
>> Thanks,
>>
>> Sunny
>>
>> On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> sunny mishra wrote:
>>
>> Hi all,
>>
>> Is there anyway I can generate the .gro file from .top file
>> without using the command pdb2gmx and editconf?
>>
>>
>> A .top file is a topology - atomic descriptions; a .gro is a
>> coordinate file. They are unrelated and therefore cannot be
>> inter-converted.
>>
>> -Justin
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
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