Re: FEP on charged residue mutation

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sat Nov 22 2008 - 12:27:19 CST

Dear Sebastian,
That is correct, there is no need for a special hybrid residue if
entire molecules are appearing or vanishing.
Now, which kind of free energy difference exactly do you want to estimate?
Jerome

On Sat, Nov 22, 2008 at 1:14 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> wrote:
> 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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