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

[Justin A. Lemkul]

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>> 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> | (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

========================================