sunny mishra wrote:
Hi,
Thanks a lot for the quick reply. I want to position restrain the head
group atoms of CG DSPC but I am not sure about the head group molecules
in DSPC. Can you please tell me how to figure out the head group atoms
Presumably there is a structure of DSPC somewhere you can refer to. I would
think you should know the chemical features of the structures they are
simulating before diving right in blindly :)
or molecules. Also, when you say co-ordinate file then you mean .itp
file for the lipid right?
No, I mean coordinate file. An .itp is a topology.
-Justin
Thanks
On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
sunny mishra wrote:
Dear All,
I am trying to run the Position Restrained simulation for the
Coarse Grained DSPC bi-layer. However, I am quite confused that
how to generate the position restraint file for the CG atoms in
lipid. Is there a difference between the position restraint file
for the fine grained and coarse grained structures. Please let
me know how to generate the position restraint file for Coarse
Grained DSPC bi-layer. Your reply for the same will be highly
appreciable.
You can generate a position restraint file for any molecule using
genrestr. Just make sure to supply it with a coordinate file for a
single molecule (i.e., not your entire bilayer), since position
restraints are applied to moleculetypes, and not global structures.
-Justin
Thanks,
Sunny
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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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