Re: [AMBER] regarding mmpbsa

From: Asfa Ali <>
Date: Thu, 1 Jul 2010 10:31:45 +0530


There are two central K+ ions which are essential and should be retained. I
am using sander and explicit solvent method for running the simulations
(even in the mmpbsa tutorial, sander is used, I don't know
how to use GB during MD runs).

Regarding the correction you mentioned for the pb errors in, I'm
too ignorant to do it.

Can you plz suggest any other way out? I was following the tutorial since I
have the latest Ambertools and Amber9 package but I'm ending with errors.

On the other hand I tried to do in Amber9. There it's showing:

Died at /soft/amber9//src/mm_pbsa/ line 498, <PDB> line

Can you plz tell me the radius of K+ ion so that I can add it in the* file.
Plz help.

Thanx a lot...

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Received on Wed Jun 30 2010 - 22:30:03 PDT
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