[gmx-users] Re:pdb files and force field

Bhawana Gupta bhawana.gupta2010 at gmail.com
Thu Apr 9 09:23:58 CEST 2009

hello sir,

Thankyou for the reply.
The pdb file i had taken from the TINKER is the one where force field used
is oplsaa.

when i use this file in gromacs.it give error of atom type.
when i had gone in top folder which is in gromacs where all the force fields
are defined.
its written that you must define it yourself.
i don't know how to do that.

My peptide is Ace-Arg-Pro-Val-Thr-NMe
its giving error in the atom type of NMe(N-methyl)
i had changed its name from NMe to NAC as defined in the forcefield.
But another error came for Ace i.e. its CH3 atomtype not found.

Tell me want to do.
Should i send you my pdb file???
So that u can help me better.

with regards
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