On 8/19/13 6:27 AM, Aditya Padhi wrote:
Dear Gromacs Users,
I am new to Gromacs. Recently, I started working with Gromacs. I
want to study the mechanism of interaction of certain peptides that are
known to interact with membranes such as DOPC, POPC and so on. I have two
sets of peptides; out of which, one set of peptides are known to penetrate
the membrane while the behavior of another set of peptides with the
membrane is not known.
It would be really helpful if you can suggest me an appropriate
tutorial on these lines. The most common query I have is to how to place
and allow a peptide to cross or interact with the membrane? Shall I use VMD
or any other software for this?
Please let me know your response.
There are many ways of placing molecules at specific locations within the unit
cell. editconf can do this. There is no tutorial specifically for what you are
trying to do, but you can generally get some guidance from:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
Note that you do not necessarily have to use a Gromos96 force field for your
simulations; other force fields may perform better. Do your homework first!
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html
The example editconf commands here should be instructive.
-Justin
Thanking you,
Regards
Aditya.
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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