On 12/28/12 2:24 AM, Shine A wrote:
sir,
I am studying the dynamics of membrane protein.I want to use amber force
field.Then what changes should I make in the ffnonbonded.itp and
ffbonded.itp?Is it similar as in Justin manual?Is it necessary to convert
C6 and C12 values in lipid.itp(for gromos) to values in terms of sigma and
epsilon(for amber).
The parameters in lipid.itp are not compatible with the AMBER force fields.
There are published parameters for several lipid types using AMBER/GAFF
parameters. You should look into those. If the lipid parameters require new
nonbonded or bonded parameters, then those need to either be declared in the
force field itself or in the lipid topology.
-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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