Thanks for the reply Dr. Ray Luo
________________________________
From: Ray Luo <ray.luo.uci.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 11 May, 2009 11:44:20 PM
Subject: RE: [AMBER] Error in binding energy (MM PBSA)
Dear Vikas,
I recommend that you carefully go through the amber tutorial for beginners.
The tutorial is designed to help you set up and conduct a simulation. It
also teaches you how to check your simulation to spot any potential
problems.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Vikas Sharma
Sent: Monday, May 11, 2009 1:08 AM
To: amber
Subject: Re: [AMBER] Error in binding energy (MM PBSA)
Dear Dr. Ray Luo..
Thanks for the reply..
I shall do the simulations again, but what sort of changes should i
try...like should i change the size of the TIP3P box(i chose 8.0 last
time)..or any other specific changes..i followed the anber tutorial for MM
PBSA..
Thanks...
________________________________
From: Ray Luo <ray.luo.uci.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, 10 May, 2009 7:09:05 AM
Subject: RE: [AMBER] Error in binding energy (MM PBSA)
Vikas,
Well if that's the case, you'll have to redo the explicit water simulation
then ...
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Vikas Sharma
Sent: Saturday, May 09, 2009 12:19 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Error in binding energy (MM PBSA)
Dear Ray Luo..
Thanks for the reply....
I checked the movie of my production runs and found that the bonds have
stretched towards the edge of the water box...
what should i do now?
thanks
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Received on Wed May 20 2009 - 16:09:55 PDT
