On 12/16/12 11:55 PM, Shine A wrote:
Sir,
I studying the dynamics of membrane proteins.First I did a 20 ns
simulation using GROMOS96 53a6.This force field cause some problems in the
helical part of the protein.Now I am trying to do the same simulation with
opls-aa force field.Is the changes I should have to do in ffnonbonded.itp
and ffbonded,itp is same as in the justin manual?
The concept is the same, but the actual information will be very different. As
I recall, there are OPLS-AA lipid parameters somewhere out there, but I've never
used them personally. One can also implement a hybrid approach wherein the
Berger lipids can be made compatible with OPLS-AA. There's a link to that
method in my tutorial and it has been discussed on the mailing list at length.
For what it's worth, the helical instability is almost certainly due to the use
of 53A6, which is known to over-stabilize extended configurations and
under-stabilize helices.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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