[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
>>
>>    ========================================
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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
>
> ========================================
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