[gmx-users] Topology of Graphite Oxide

[Justin Lemkul]

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

-- 
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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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