Re: [AMBER] regarding mmpbsa

From: Dwight McGee <>
Date: Thu, 1 Jul 2010 10:09:20 -0400

Hi Asfa

In order to change the pb input: Go $AMBERHOME/src/mmpbsa_py
Use your favorite editor and open up
Search for the string: *def pbmdin_old*
You should see the following:

   ntb=0, cut=999.0, nsnb=99999,
   imin=5, maxcyc=0, cutcap=-1, xcap=0,
   ycap=0, zcap=0, idecomp=0, ntpr=1,
   ivcap=0, ntmin=2, igb=10, """)
you need to remove the following variables: *cutcap*, *xcap*, *ycap*, and *
Save the changes and copy the file to the $AMBERHOME bin

NOTE: if you don't have write permissions use the {-use-mdins} option

On Thu, Jul 1, 2010 at 1:01 AM, Asfa Ali <> wrote:

> Hi,
> 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
> 718.
> Can you plz tell me the radius of K+ ion so that I can add it in the*
> file.
> Plz help.
> Thanx a lot...
> Asfa.
> *
> _______________________________________________
> AMBER mailing list

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
"Problems cannot be solved at the same level of awareness that created
               Albert Einstein
AMBER mailing list
Received on Thu Jul 01 2010 - 07:30:04 PDT
Custom Search