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<jalem...@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
========================================
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