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.
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