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
