[gmx-users] water.pdb file

[sunny mishra]

Hi Justin,

That sounds perfect to me. I think using the water.mdp file and
water.top file I can create my own water.gro file including any number
of molecules i guess.

I realized one more thing that I need to create my own protein.ssd
file from do_dssp program I guess,  because in the tutorial I was
given these files already but for my own protein I have to create one.
In the MARTINI tutorial they have provided me the seq2itp.pl script
which can convert my 1K4C.seq file to 1K4C.itp file but for that I
need 1K4C.ssd file. The command is as:

seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp

I don't know how to create 1K4C.ssd file now because when I try to
create it using do_dssp it asks me to generate the topol.tpr file and
I cannot generate that before simulation. Do you have any idea about
this?

Sunny

On Mon, Aug 10, 2009 at 6:31 PM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
>
>
> sunny mishra wrote:
>>
>> Hi Justin,
>>
>> Thanks for the expedient reply. In the MARTINI tutorial they have
>> provided two water.gro files one for lipids and the other for
>> proteins. Protein water molecule file consists of 10800 atoms of water
>> and the lipid has 400 atoms. So even if I simulate any protein
>> structure after converting that to CG, can I use the same water.gro
>> file for protein always?
>>
>
> I don't know about different water files based on the system; that seems a
> bit arbitrary.  I'm referring to the one single water.gro file here:
>
> http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
>
> If there are differences between using the water structure with proteins and
> lipids, any changes are likely reflected in the force field, version 2.0 for
> lipids, and version 2.1, which is the extension to proteins, if there is a
> difference at all.  Any reasonable equilibrated box of water will probably
> suffice; your equilibration will likely take care of any differences, if
> they exist.
>
> -Justin
>
>> Sunny
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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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