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.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Sep 28 2008 - 05:10:18 PDT
