Re: FEP on charged residue mutation

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sat Nov 22 2008 - 12:14:57 CST

Dear Jerome,

:-)

let's assume I was wrong, and I need free energy values, have a large
system and want to do this:

prot(Arg)+env.+1*H2O =>prot(Ala)+env.+1*SOD

In the fep file, I already took care of the "R2A" entry.
Is it possible, in addition, simply adding a SOD entry on top of a water
molecule, such that:

ATOM 68967 SOD SOD 15.792 13.486 -32.681 1.00 1.00 SOD
ATOM 68968 OH2 TIP3W9241 15.792 13.486 -32.681 1.00 -1.00 WT8
ATOM 68969 H1 TIP3W9241 15.621 12.544 -32.685 1.00 -1.00 WT8
ATOM 68970 H2 TIP3W9241 15.814 13.730 -33.606 1.00 -1.00 WT8
,where I use the B column for the dual-paradigm and put constraints on
the SOD and the OH2 atoms?

I ask because I want to make sure I e.g. don't need to define my own
"SOD2WAT" residue type.

Thank you so much,
Sebastian

Jerome Henin wrote:
> Hi Sebastian,
>
>
>> I am just interested in a final structure, not any exact free energy values.
>>
>
> Oh, then you might not need FEP at all... did you try just setting up
> the mutant (carefully) and simulating it right away? In any case, you
> don't need a thermodynamic cycle.
>
> Jerome
>

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