OK, so I should decrease initial restrained distance between ligand and some
active site residue during simulation in case of transport from solvent to
the pocket (or increase distance in case of transport from the pocket to
push ligand away). And certain direction of transport isn`t specified with
the hope that ligand will find its way by itself.
Am I right?
Thanks!
On Fri, Mar 13, 2009 at 4:45 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Look at the amber 10 manual, under Steered molecular dynamics (page 108).
>
> Also look, under the $AMBERHOME/test/jar and jar_multi directories for
> examples
>
>
>
>
> Dmitri Nilov wrote:
>
>> Thank you for answer, so could you advise me alternative appropriate
>> method
>> in Amber10 to explore
>> ligand transport from solvent into active site or to push ligand out of
>> the
>> pocket?
>> I suppose, that similar way is to restrain ligand position using "position
>> restraints" method
>> with reference coordinates. But I know that position restraints are not
>> quite appropriate for constant pressure simulations.
>>
>>
>> On Thu, Mar 12, 2009 at 9:46 PM, Adrian Roitberg <roitberg.qtp.ufl.edu
>> >wrote:
>>
>> Short answer, NO there is no such thing in the SMD code.
>>>
>>> However, it does mot matter.
>>> What you need to do is PUSH the ligand out of the pocket.
>>>
>>> This is substantially more physical that pulling from outside.
>>>
>>> Adrian
>>>
>>>
>>> Dmitri Nilov wrote:
>>>
>>> Hello!
>>>> Is there facility to pull ligand from active site in Amber10?
>>>> I mean steered molecular dynamics when external harmonic force is
>>>> applied,
>>>> in other words a "spring" connected
>>>> to ligand is retracted in certain direction with constant velocity.
>>>> I can`t get clear answer from Manual and mailing list. Could you help
>>>> me?
>>>>
>>>> Dmitri Nilov,
>>>> Lomonosov Moscow State University
>>>> _______________________________________________
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>>>>
>>>>
>>>> --
>>> Dr. Adrian E. Roitberg
>>> Associate Professor
>>> Quantum Theory Project
>>> Department of Chemistry
>>>
>>> Senior Editor. Journal of Physical Chemistry
>>> American Chemical Society
>>>
>>> University of Florida PHONE 352 392-6972
>>> P.O. Box 118435 FAX 352 392-8722
>>> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
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>>
>>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Mar 15 2009 - 01:09:40 PDT
