My guess is you are looking for cpptraj or MMPBSA input help. Likely COM
is center of mass, REC is receptor, LIG is ligand, but what RES is I
can't guess, likewise PRI, and why COM,REC,LIG are in the same list
against PRI is tantalizing but beyond my imagination, perhaps not input
to a program but some kind of general nomenclature used by chemists.
Here's an advanced tutorial on free energy decomposition if it helps:
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
Regards,
Bill
On 4/14/17 10:47 PM, nagakumarb.ccamp.res.in wrote:
> Dear Bill,
>
> Thank you for the response, I would like to calculate residual
> decomposition for covalent inhibitor which i have connected to the residue
> 208 (total number of residues 240).
>
> As this covalently modified residue in middle of the protein, how can i
> declare "COMREC", "COMLIG", "RECRES", "{COM,REC,LIG}PRI" and
> "{REC,LIG}MAP".
>
> Covalently modified residue is reduntant in REC if i consider it as LIG,
> I dont have any clue how to separeate this residue for decomposition
> calculations.
>
> Let me know if the description is not clear, i will try again.
>
> Regards,
> Kumar
>
>
>
>> For what it's worth, I as a semi-layman don't know exactly what you are
>> talking about, which may overlap with why your question hasn't been
>> answered.
>>
>> Bill
>>
>>> I am wondering how to declare "COMREC", "COMLIG", "RECRES",
>>> "{COM,REC,LIG}PRI" and "{REC,LIG}MAP"
>>
>> On 4/14/17 10:02 PM, nagakumarb.ccamp.res.in wrote:
>>> Hello,
>>>
>>> This is regarding my earlier residual decomposition related question...
>>> as
>>> i haven't get any solution to this issue, i assume this problem is
>>> technical challenge and not possible to solve. I will still wait for
>>> responses if someone already dealt such problems.
>>>
>>> Regards,
>>> Kumar
>>>
>>> -----------------------------
>>>> Hello,
>>>>
>>>> Can someone help me to solve this residual decomposition problem... I
>>>> have
>>>> posted few days back and waiting for help. I am attaching my earlier
>>>> message here.
>>>>
>>>> Thanks in advance.
>>>>
>>>> Regards,
>>>> Kumar
>>>> -------------------------
>>>> Hello,
>>>>
>>>>
>>>> I am working on a system (around 240 residues) in which ligand
>>>> covalently
>>>> bound to a cysteine residue. This cysteine residue is in middle of the
>>>> protein structure (residue 208). I have created new residue (Cys +
>>>> covalent
>>>> ligand) using xleap and i completed the simulation successfully.
>>>> Everything looks normal for visual and initial analyses.
>>>>
>>>>
>>>> Now i am trying to do residual decomposition for this simulation where
>>>> i
>>>> am facing some issues.
>>>>
>>>>
>>>> Can someone help me to generate "extract-coord.in" and "reswise.in"
>>>> files
>>>> for this case?
>>>>
>>>>
>>>> I am wondering how to declare "COMREC", "COMLIG", "RECRES",
>>>> "{COM,REC,LIG}PRI" and "{REC,LIG}MAP"
>>>>
>>>>
>>>> Please help me this regard and let me know if you need any further
>>>> information to solve this puzzle.
>>>>
>>>>
>>>> Regards,
>>>>
>>>> Kumar
>>>>
>>>
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>
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Received on Fri Apr 14 2017 - 23:30:03 PDT
