AMBER Archive (2009)

Subject: RE: [AMBER] Error in binding energy (MM PBSA)

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon May 11 2009 - 13:14:20 CDT

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_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_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_at_uci.edu>
To: AMBER Mailing List <amber_at_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_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_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

________________________________

      Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo!
Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox
_______________________________________________
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