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

[Justin A. Lemkul]

sunny mishra wrote:

Alright sounds good to me. In order to make it sure once again....I have 
to do something like this...

awk -f atom2cg.awk 1K4C.pdb > 1K4C_cg.pdb

and then....to get the .gro file....

genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro


Or you can use editconf, but genbox will also work.

and then......

grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10

AM I CORRECT?


The only way to know is to try.  In theory, yes, the above should work.

-Justin

Sunny


On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    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>
        <mailto: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>>
               <mailto: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>
        <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> <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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