[gmx-users] quality of a topology and pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 28 16:08:02 CET 2012

Lara Bunte wrote:
> Hi
> If you have a good parametrization of a molecule and it's pdb file and you
> use pdb2gmx for getting a topology, will the topology alway be finished?

If you're dealing with a new residue that you've introduced into the .rtp file, 
the topology is only as good as the completeness of the .rtp file.

> It is usual to fix something in the topology file after pdb2gmx or are
> necessary additions in the topology a hint for a bad or even wrong
> parametrization in the force field?

Making changes, additions, or deletions to a pdb2gmx-generated topology would be 
unusual.  It's not likely a consequence of bad parameterization, rather bad 
construction of the necessary input files.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list