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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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