[gmx-users] water.pdb file

[Justin A. Lemkul]

sunny mishra wrote:
> 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?
> 

The .ssd file is just a text file with codes for secondary structure elements. 
I can think of two ways to generate it:

1. You can use the standalone dssp executable on the starting .pdb file to 
generate an analysis of secondary structure.

2. If your .pdb file is from the RCSB, it probably contains HELIX and SHEET 
entries that you can use to determine the secondary structure.

After either (1) or (2) above, create the .ssd file yourself.  A little tedious, 
potentially a lot of typing, but I don't know how else to do it.

-Justin

-Justin

> 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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-- 
========================================

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

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