Hi Kumar,
Are you wondering how to *prepare* prmtop's for the cases below? The
choice of using modified residue or not is beyond me, but I might be
able to answer specific questions on prmtop preparation. Intuitively I
would think that if there is a choice you might need both, which could
keep you busy until expertise arrives.
Regards,
Bill
On 4/14/17 11:32 PM, nagakumarb.ccamp.res.in wrote:
> Dear Bill,
>
> Thank you for sharing information and links. I have done residual
> decomposition sucessfully in several projects without any trouble. But in
> those instances i have dealt with either ligand or peptide. Such case are
> stright forward as we consider them as separate entities in simulations
> therefore extracing coordinates from complex simulations and running
> resudual decomposition by MM/GBSA is stright forward.
>
> Now in covalent inhibitor case i am trying to extract coordinates
>
> Here is input
>
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1 (I assume this is corrent for covalent modified
> residue)
> #
> COMPT ../com-sol1.prmtop
> RECPT ../rec.prmtop (How to decalre this with modified
> residue or without)
> LIGPT ../lig.prmtop (How do decare the modified residue??)
>
> Similarly how to declare values in MM/GBSA residual decomposition input
> file??
>
> # COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
> # COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
> # RECRES - Residues in the receptor molecule.
> # LIGRES - Residues in the ligand molecule.
> # {COM,REC,LIG}PRI - Residues considered for output.
> # {REC,LIG}MAP - Residues in the complex which are equivalent to the
> residues
> # in the receptor molecule or the ligand molecule.
> #
> DCTYPE 2
> #
> COMREC 1-241
> COMLIG 208-208 (modified residue... is it correct
> declaration??)
> COMPRI 1-240 (These declaration is conflict with ligand)
> RECRES 1-240 (This declaration is conflict with ligand)
> RECPRI 1-240 (This declaration is conflict with ligand)
> RECMAP 1-240 (This declaration is conflict with ligand)
> LIGRES 1-1
> LIGPRI 1-1
> LIGMAP 208-208
>
> I am wondering how to declare the above values to complete the residual
> decomposition calculations.
>
> Regards,
> Kumar
>
>> 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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Received on Sat Apr 15 2017 - 00:00:02 PDT
