AMBER Archive (2009)

Subject: Re: [AMBER] SMD in Amber10

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Fri Mar 13 2009 - 03:52:26 CDT

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