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

sunny mishra mishra.sunny at gmail.com
Wed Aug 19 01:54:41 CEST 2009


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

and then......

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

AM I CORRECT?

Sunny


On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul <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>> 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>>> 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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>>
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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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