targeted MD as implemented in AMBER is not appropriate
for this problem. it can only increase or decrease an
RMSD with time, and for your case you don't want the protein
rmsd to go up, you want the distance to the ligand to rise.
I think that what you need to use is a distance
restraint and increase the value of the distance with time.
this will only show you the dynamic process, of course
as you suggest you will need to calculate a PMF (I suggest
umbrella sampling) for the free energy profile.
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.stonybrook.edu
===================================================================
----- Original Message -----
From: "Lishan Yao" <yaolisha.pilot.msu.edu>
To: <amber.scripps.edu>
Sent: Thursday, July 24, 2003 3:25 PM
Subject: AMBER: PMF calculation
> Hi there:
> I want to pull one ligand out of a protein. At first, I use Target MD
> in amber7. It seems that it doesn't work well. For example, it is much
> slower than a common MD simulation. And I couldn't use this method to do
> simulation in solution. So now, I want to use PMF (potential of Mean
> Force) method. Do you have any recommendation of good reference papers
> about such kind of simulation done by using amber?
>
> Best,
> Lishan
>
> --
> Lishan Yao <yaolisha.pilot.msu.edu>
> MSU
>
>
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Received on Mon Jul 28 2003 - 16:53:01 PDT
