On 3/7/13 3:36 AM, zhhxu wrote:
Hi users:
I want to run a simulation of adsorption of protein on graphite oxide(GO) which
is oxidized at random and
is near 80% coverage by hydroxyl and epoxyl group.
My first question is how to generate a topology filefor GO. Previous to search
solution to this problem in
this forum, I had tried to make a topology for GO use g_x2top with command:
g_x2top -f input.pdb -nopbc -r outputname -o outputname.
But g_x2top did not work fine(fine for prestine graphite) and gave error messages like
"Can not find forcefield for atom .. "
The .n2t files provided with the (few) force fields in Gromacs are rather
inflexible, so you will probably need to modify them to suit your needs.
My second also is about definition of improper dihedral in opls-aa. Whether it
is validate to assign a improper
dihedral for a central sp2 carbon atom with three other bonded atoms no matter
of what is type of other
three atom? I have gotten (mentioned above) a topology file of pristine
graphite for opls-aa with
g_x2top(the command is similar to above), but the topology file did not
include any improper dihedral.
g_x2top doesn't write impropers, so you have to manually add them if needed.
Assignment of proper parameters should be done based on analogous functional
groups present in the force field or by a suitable derivation protocol.
-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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