Re: Oxidized cysteine parameters for CHARMM36

From: Brian Radak (
Date: Fri Sep 30 2016 - 09:35:08 CDT

I would look at the Force Field Tool Kit (FFTK) packaged with VMD and/or
General Automated Atomic Model Parameterization (GAAMP) hosted here at ANL.

The latter is more for small molecule parameterization while the former
is more for compatibility with CHARMM (I believe, I hope I'm not
misrepresenting it).

Just my opinion - sulfur is generally NOT well covered in the protein
and nucleic acid force fields. There is probably a trade off in the
properties that will be well reproduced and you might need to think a
bit about what you want your simulations to tell you. I had a painful
experience trying to work with phosphorothioates a few years back and
ended up scrapping the whole project (although that was also because my
thesis was complete without that project).


On 09/30/2016 08:40 AM, Gergely Gyimesi wrote:
> Dear NAMD users,
> I am currently on the lookout for parameters for oxidized cysteine
> (cysteine sulfenic/sulfinic/sulfonic acid) that can be used with
> CHARMM36. So far I have only found SwissSidechain, but it doesn't have
> them, and some other parameters for other force-fields. I was
> wondering if anyone has come across anything like that, I would be
> grateful for any hints.
> Best regards,
> Gergely Gyimesi

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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