Thanks Bill, I will wait for responses and let you know if i get answer.
Regards,
Kumar
--------------
> 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 - 05:30:03 PDT
