Hi,
I think if you set up a thermodynamic cycle you can do it. One leg of
the cycle will be the mutation in gas phase, i.e., the inner and outer
dielectrics will be 1, then repeat it with the outer dielectric adjusted to
80. This is sort of turning the FEP cycle on its "head" (actually on its
side).
Try it, it may work.
Rami
On 1/9/11 7:29 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> Hello,
>
> MMPBSA.py cannot do this yet, but will be able to in the future (in the form
> of alanine scanning). mm_pbsa.pl can do this, I think (in the form of
> alanine scanning), but I've never done it that way and couldn't say how.
>
> Good luck,
> Jason
>
> On Sun, Jan 9, 2011 at 2:21 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
>
>> Dear amber users,
>>
>> Currently, I want to calculate the mutational energies on the protein
>> without binding ligands. Can MM-PBSA do this job? There is no problem to
>> calculate the mutational energies binding ligands using MM-PBSA. But in some
>> cases, people are really interested in calculation of the mutational
>> energies of the protein to investigate the significance of some residues to
>> the stability of the protein.
>>
>> Thanks for you help in advance!
>>
>> Rilei Yu
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 09 2011 - 08:30:02 PST
