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
>>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 14 2017 - 23:00:02 PDT
