[gmx-users] Topology of Graphite Oxide

[zhhxu]

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 .. "

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.

  I will appreciated you for giving any advice.

       
sincerely
zhhxu PhD student
Institute of Process Engineering, Chinese Academy of Sciences,
Department of Biochemical Engineering.