AMBER Archive (2009)

Subject: Re: [AMBER] SMD in Amber10

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Mar 13 2009 - 10:01:31 CDT

Almost right, but with some details.

Remember that the moving restraint is 'spherical', in the sense that
only the distance is restrained, but not the angles.

When pulling something into the protein, you must start somewhere close
to the mouth of the ligand pocket. If you start far away, there is an
almost zero chance that the ligand would find it way around to the entry
site.

When pushing out, such care is not needed. The ligand will basically get
out on its own. Even if it starts going 'the other way' it will hit the
protein and move out. Just do some short runs to figure out the force
constant values and the speed at which you will move the restraint
before going too far.

Adrian

Dmitri Nilov wrote:
> 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_at_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_at_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
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER_at_ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>> --
>>>> 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_at_qtp.ufl.edu
>>>>
>>>> _______________________________________________
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>>>>
>>>> _______________________________________________
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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_at_qtp.ufl.edu
>>
>> _______________________________________________
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>>
> _______________________________________________
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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_at_qtp.ufl.edu

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