[gmx-users] CR atom name CHARMM27 ff

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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