[gmx-users] CR atom name CHARMM27 ff
jalemkul at vt.edu
Wed Oct 4 13:53:28 CEST 2017
On 10/4/17 7:30 AM, Sergio Manzetti wrote:
> Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in the charm27 ff atomtypes. What is the correct name for this?
If you're getting a force field file that has atomtypes that are not present in
the parent force field, you should immediately be suspicious of compatibility.
CR is indeed not a normal CHARMM atom type. I don't know what "protparam.org" is
(and that website doesn't load anything for me) but whatever you're using needs
to clearly explain what it's doing to generate parameters.
If you want to be safe in generating CHARMM topologies, use cgenff.paramchem.org
- it is 100% compatible with the latest CHARMM36 force field and always provides
all necessary parameters, as well as clear indications of areas needing
refinement in the topology. That, to me, is the gold standard of parametrization.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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