[gmx-users] query regarding itp file

[soumadwip ghosh]

Thanks Mark for the prompt reply. I can probably make the posre files if
required now. But I would be relieved if someone sheds light on the first
question that if I already have an .itp file is is necessary to make an
entry for the atoms in the aminoacid.rtp file of the corresponding force
field? I did not do pdb2gmx to generate the topology of the graphene
molecule since I obtained the same from PARAMCHEM and the atom types used
for graphene are CA and HP which are consistent with some literature. Do I
need to modify my aminoacid.rtp file or can I be assured that proper
interactions would arise since I am using A BETTER FORCE FIELD (CHARMM 27)
for a longer MD simulation (200ns) as per the suggestion by Justin. As far
I am concerned the outputs of PARAMCHEM are reliable. I am confused whether
I have provided the correct .itp file and whether the expected interaction
would arise or not.

Waiting for your reply.

Regards,
Soumadwip
Research Fellow
IITB
India