Re: FEP on charged residue mutation

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sat Nov 22 2008 - 13:48:14 CST

Dear Jerome,

for now, in

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

I'd like to estimate the free energy difference for

prot(Arg)+env.=>prot(Ala)+env. (II)

Because my system is large, I plan to do

env.+1*H2O =>env.+1*SOD (III)

(in a simple small water box) and subtract its free energy difference from the one in (I), to get the one for (II).

Am I being too disrespectful of real nature? ;-)

Thank you,
Sebastian

PS: I'll try try to put the "1*SOD" as far as I can from the protein

Jerome Henin wrote:
> 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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