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.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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Received on Sun Jul 13 2008 - 06:08:08 PDT
