[gmx-users] regarding pdb2gmx

[soumadwip ghosh]

Thank you very much for your help Justin. I really appreciate

I would like to bother you for one last time ( as of now ;). So, if I
am dealing with a non-trivial molecule like CNT or some
polyelectrolyte and I mainly intend to demonstrate the non-bonding
interactions with some nucleic acids (say a CNT-dsDNA ) interaction,
it appears to me that I dont need to care about the DNA topology even
if it lacks the said parameters but I do have to care about these
while updating the cnt.itp files since grompp complains about the
missing parameters in the cnt.itp file. If one does not write the [
atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and
misses out the sigma and epsilon terms I think it underestimates the
non-bonding energy terms of interaction between DNA bases and CNT
atoms in the md.edr file to some extent. I will appreciate your
opinion on this statement.
Thanks for your time in advance

Soumadwip
Research Fellow
IITB
India