AMBER Archive (2008)

Subject: Re: AMBER: calibration of constant pH simulations

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Wed Apr 30 2008 - 23:02:55 CDT

I have a related question regarding the constant pH simulation.

Has anybody reproduced the results for lysozyme given in the J.Comp.Chem. paper (Mongan, Case, McCammon)?

We have been trying this with the protocol mentioned in the paper and the results differ quite a bit.

I help appreciate any help.

 Pradipta

>>> Adrian Roitberg <roitberg_at_qtp.ufl.edu> 30/04/08 11:35 PM >>>
Lilian.
Not that I know off, but...

We are running tons of these simulations using exactly the setup you
mentioned (ff99SB/igb=5) using the default internal parameters for
constant pH as they came in amber.

We can reproduce the pKas for the reference compounds used for the
original parametrization to within 0.01 pKa units. This tells me that if
you try to reparametrize, you will spend a very large amount of time
(you must do full free energy perturbation, etc) for no real results.

This is not a completely unexpected result. After all, ff99SB is simply
a refit of the torsional potential on top of the ff99 set, using the
same charges. For the reference compounds (single ionizable aminoacids,
capped) the effect would be minuscule.

Cheers
a.

Lillian Chong wrote:
> Dear Amber Users,
>
> I have a question about the constant pH simulations approach in AMBER
> 9. I would like to use ff99SB along with the igb=5 GB model for these
> simulations. Has anyone calibrated the constant pH simulations
> approach for use with this force field and water model?
>
> If not, we would be happy to do it and make the parameters available.
>
> Best,
> Lillian
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
============================================================================

To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu