[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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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