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

[sunny mishra]

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

My topology file looks like this

; Include forcefield parameters
#include "martini_v2.1.itp"

; Include protein
#include "1K4C.itp"

[ system ]
; Name
Membrane Protein

[ molecules ]
; compound    # mols
Protein               1

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 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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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