Hi Jason,
Thank you. I was mainly concerned that the frcmod format appears to support
atom classes with a maximum of two letters (which would make hundreds of
atom classes unwieldy), but your response sounds like this isn't a problem.
I'm curious, how is this handled? Can I have multiple atom classes that use
the same two letters (they just get used for different residues)?
Thanks,
- Lee-Ping
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Tuesday, June 10, 2014 10:47 AM
To: amber.ambermd.org
Subject: Re: [AMBER] Side chain and backbone-specific parameters.
On Tue, 2014-06-10 at 10:25 -0700, Lee-Ping Wang wrote:
> Hi everyone,
>
>
>
> I'm working on some new protein force fields which have distinct
> backbone / sidechain parameters for different amino acids. My
> parameterizations are done using Gromacs, which allows atom-specific
bonded interactions (i.e.
> overriding the values that come from atom classes).
>
>
>
> I don't see this functionality in AMBER, and it looks like the
> ff99sb-ildn and ff12sb models have extra atom classes to accommodate the
extra torsions.
> Since I plan to port my force fields to AMBER, I'd like your advice on
> how to do this most effectively.
>
>
>
> What is the best way to implement residue-specific backbone and side
> chain parameters? Should this be done by adding many atom classes?
Yes.
> Is it even
> possible to add on the order of 100 atom classes?
Yes. tleap should create a condensed set of vdW atom classes by combining
atoms that have the same vdW parameters into a single class, but should have
no problems handling a very large number of atom classes for parameter
assignment.
Indeed, loading the ff14SB force field with GLYCAM, lipid14, and GAFF force
fields loads ~200 atom types already.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 11:00:04 PDT
