AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Vikas Sharma (
Date: Wed Jun 03 2009 - 09:24:14 CDT

Dear Dr. David Case,
 Thanks for the reply...I have fixed that problem...

i am doiong the the binding free energy calculation for another ligand...

when i run : binding_energy.mmpbsa > binding_energy.log
i get the following error:

/opt/amber10/exe/sander -O -i -o sander_com.1.out -c
/home/bharatam/amberresults_w/amberresults_ligand/snapshot_com.crd.1 -p
/home/bharatam/amberresults_w/amb31/prot_lig.prmtop not successful

how can i fix this one?

thank you

From: David A. Case <>
To: AMBER Mailing List <>
Sent: Wednesday, 3 June, 2009 5:13:54 PM
Subject: Re: [AMBER] Error in MM PBSA

On Wed, Jun 03, 2009, Vikas Sharma wrote:
> if i need to do only bugfix21 then....should i copy the whole file to
> amber10/src/mm_pbsa/molsurf.c and run as:

If you only want to apply bugfix.21, then just download the bugfix.21 file.
Note that patch files are human-readable -- you can edit the files by hand if
you have difficulties with patch.


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