[gmx-users] query regarding itp file

[soumadwip ghosh]

Hi all,
       I have some general doubts about the use of an itp file built by
some software. I am studying the dynamics of a DNA in presence of a
graphene sheet. I am using now the CHARMM27 force field and have obtained a
graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon
atoms and the terminal hydrogen atoms of the graphene sheet have been taken
into account according to the standard CHARMM directory. Now, do I need to
modify my aminoacids.rtp file in order to account for the atoms in the PDB
file? I have not done any pdb2gmx so do I really need to do that step? The
atom types in the .itp file provided by the PARAMCHEM has CA and HP atoms
which describe the graphene framework in addition to other non-bonded
parameters. The equilibration steps are running without any hitches but I
am not getting whether the proper interaction (atomistic) would arise
between graphene and DNA atoms. As suggested by Justin i've switched over
to CHARMM27 force field and am looking at atlest 200 ns of production run.
Another question is, since I have not performed pdb2gmx on graphene, I dont
have a posre_graphene file. Is it gonna create some problem later during
mdrun? I will be grateful if someone clarifies my doubts. Can I get a posre
file for graphene by some other method without doing pdb2gmx if this file
is mandatory?

Hope I'm not asking for much.

Regards,
Soumadwip
Research Fellow
IIT Bombay
India