[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

[Justin Lemkul]

On 7/2/19 12:01 PM, Pandya, Akash wrote:
> Do I still need to do this if I just want charged arginine (CARG)? Its my understanding that there are three types of arginine residues;  ARG, CARG and NARG available. I thought the amino acids are available in gromacs? Sorry if it's a silly question to ask, but I have not used the Amber FF in gromacs before.

CARG = C-terminal arginine, which is an AMBER convention. It does not 
mean "charged" arginine.

Not all force fields support zwitterions, because they are challenging 
to parametrize are not widely needed. OPLS supports zwitterionic amino 
acids, as should CHARMM and possibly GROMOS. These are all supported by 
GROMACS.

-Justin

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Justin A. Lemkul, Ph.D.
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