Re: [gmx-users] .top file from .gro file

[Justin A. Lemkul]

sunny mishra wrote:
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.


You need the awk script to generate the CG structure.  You use the atomistic 
structure to get the .ssd information - you've done this correctly.

Here is the error------------

grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10

<snip>


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.                                             


Pay attention to these notes!

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)   



Now this makes sense.  You are using an atomistic structure (1K4C.gro) with a CG 
topology.  The structure input into grompp should be the CG structure that comes 
from the awk script.

-Justin




On Tue, Aug 18, 2009 at 7:24 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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> <http://vt.edu> | (540)
        231-9080

           http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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--
========================================

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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