AMBER Archive (2003)

Subject: Re: AMBER: target MD simulation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Aug 27 2003 - 14:59:09 CDT

I would not suggest using targeted MD for pulling
out a ligand. It is hard to image a way to get that
to work. You should really use it for things specifically
related to RMSD. Otherwise, you might want to try
distance restraints, which are probably much faster.

I am fairly sure that the RMSD code could be made faster,
but again it was not designed for the purpose that
you are using it for and I suggest trying something
different rather than reprogramming it.
Carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

----- Original Message -----
From: "Lishan Yao" <yaolisha_at_pilot.msu.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, August 27, 2003 2:01 PM
Subject: AMBER: target MD simulation

> Hi there:
> I tried target MD once. I use GBSA model. Seems to me, the simulation
> is quite slow. My system is a protein ligand complex about 1000 a.a.. I
> pulled the ligand out. I talked with one of my friend. He thinks that
> each time when amber superimposes the current structure with target
> structure, it is quite expensive. So do you have any experience with
> target MD? I wonder whether I can run it faster.
>
> Best,
> Lishan
>
> --
> Lishan Yao <yaolisha_at_pilot.msu.edu>
> MSU
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu