AMBER Archive (2009)

Subject: Re: [AMBER] SMD in Amber10

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Mar 13 2009 - 08:45:39 CDT

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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