AMBER Archive (2008)

Subject: Re: AMBER: Constant pH simulation force field

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 27 2008 - 07:10:39 CDT

On Sat, Sep 27, 2008, Soonmin Jang wrote:
>
> I am trying to run constant pH peptide simulation with amber9 using GB
> solvation. As I know, the force field for constant pH simulation is ff99SB.
> But I noticed in the manual that other force field (such as ff96, ff03, etc)
> with GB solvation might be OK as long as it satisfies the pKa value of
> target titrating residues.

In principle, either ff99SB or ff03 could be used for constant pH
simulations; we don't recommend ff96 or other older peptide
parameterizations any more.

There has been relatively little testing of any of these (especially for
ff03), so you need to proceed with caution -- running constant pH
simulations is still very much a research field.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu