AMBER Archive (2008)

Subject: Re: AMBER: Constant pH with new parameters (amber10)

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sat Jul 12 2008 - 18:47:41 CDT

Dear Markus
I am not sure what you mean by 'total charge of -6' in this context.

The protonation states are pH dependent of course. You mean you run
constant pH MD at pH = 7 (let's say) and counted charge afterwards? Are
you sure the procedure is converged ?

Now, since the parameters in constant pH MD are parametrized using the
ff99 charge model (as Dave case mentioned), then you should not use the
ff03 set at all.

Moreover, if the difference in two for a charge comes from smal
differences in a couple of histidines (as I suspect), then I wold be
very careful with the results. One would be lucky to get pKa of
histidines to within one pKa unit of experiment, and that, given the
right conditions, would easily give you one charge per histidine.

One last item: please go back to the original raw data for your protein
and see if the researchers really report a charge for their system. As
far as I can tell this an almost impossible measurement to do. There are
other measurements that seem to correlate with total charge, but you
must check for your own system.

Cheers
Adrian

Markus Kaukonen wrote:
> Thank's,
> I did some testing with poplar plastocyanin and it makes clear
> difference (~2 charge) whether one used ff03 or ff99 so I conclude
> that one should use
>
> source leaprc.ff99SB
> set default PBRadii mbondi2
> loadoff constph.lib
> loadamberparams frcmod.constph
>
> In this case I obtained total charge of -6 which is closer to
> experimental one ~-8
>
> Anyone else having comments on how well constant pH reproduces
> experimental pKa values or the total charge of a protein? My
> statistics is pretty poor here.
>
> Teveisin, Markus
>
> On 7/11/08, David A. Case <case_at_scripps.edu> wrote:
>> On Tue, Jul 08, 2008, Markus Kaukonen wrote:
>>> Is it ok to set up a constant pH calculation with leap commands in Amber
>>> 10:
>>>> source leaprc.ff03
>>>> set default PBRadii mbondi2
>>>> loadoff constph.lib
>>>> loadamberparams frcmod.constph
>>> I mean, are the force fied modifications in the manual only valid when
>>> using
>>> 'source leaprc.ff99' or can one use 'source leaprc.ff03'
>> I believe that constph.lib files are based on the ff99 charges, and so would
>> not be fully compatible with ff03.
>>
>>> Is the file 'frcmod.mod_phipsi.1' needed anymore for constant pH?
>> You want to use leaprc.ff99SB. Then you don't need the mod_phipsi stuff, as
>> it is automatically included.
>>
>> ...good luck...dac
>>
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> 

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

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

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
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