AMBER Archive (2009)

Subject: Re: [AMBER] SMD in Amber10

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Fri Mar 13 2009 - 10:17:44 CDT

Many thanks!!)

On Fri, Mar 13, 2009 at 6:01 PM, Adrian Roitberg <roitberg_at_qtp.ufl.edu>wrote:

> 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
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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