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

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 19 02:02:38 CEST 2009



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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto: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>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto: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> <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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