Thanks Jason / Bill
Your answers generated a couple of additional questions
1. Re Bill's answer
I assume that I would have to set the strip_mask to remove all waters but the one that I'm interested in. Looking at the manual I fail to see what is the syntax for this operation. My molecular viewer shows that the HOH in question is numbered as molecule 2952.
Would a syntax like the one below work?
Input file for running PB and GB
&general
endframe=50, verbose=1,
strip_mask=WAT2952
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
2. Re jason's answer
Am I correct to assume that you mean that I need to strip manually the solvated_prmtop from all waters and ions except my water of interest? If this is the case, how does one work the numbering, e.g. identify the atoms of HOH 2952?
Apologies if the above is trivial but I'm relatively inexperienced.
Best regards
George
On Feb 15, 2011, at 6:03 PM, Jason Swails wrote:
> Hi George,
>
> As a supplement to what Bill said, commas are not permissible in input
> variables in the current release. The upcoming version does not suffer from
> this limitation, so it will be easier to define masks then.
>
> Another option is to pre-process your trajectory yourself, manually removing
> all of the waters you don't want and keeping those that you do. Then just
> set the strip_mdcrd variable to 0 to avoid stripping everything and just
> supply your complex_prmtop, mdcrd, and receptor and ligand_prmtops.
>
> Hope this helps,
> Jason
>
> On Tue, Feb 15, 2011 at 11:57 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> You will have to explicitly set the strip_mask variable in the MMPBSA.py
>> input file. You will have to define the mask to strip out all the water
>> molecules you do not want, but specifically keep the residue number of the
>> one water molecule you want to keep. You can read about the details of how
>> to define the residue masks in the manual.
>>
>> Good luck!
>>
>> -Bill
>>
>> On Tue, Feb 15, 2011 at 11:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> Hi everybody,
>>>
>>> I understand that MMPBSA.py strips all HOH molecules (?) and ions from
>> the
>>> original trajectory. In my case, an individual HOH molecule contributes
>> to
>>> the binding of the ligand to the receptor. This is in accordance with the
>>> corresponding crystallographic model.
>>>
>>> Is there a way of keeping this HOH molecule in the trajectory files? I
>>> would like to find out the contribution of this HOH molecule to delta G
>> and
>>> delta S.
>>>
>>> I'd be grateful for any advice on how to go about this issue.
>>>
>>> Best regards
>>>
>>> George
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Feb 15 2011 - 10:00:04 PST
