AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Vikas Sharma (
Date: Wed Jun 03 2009 - 01:46:03 CDT

Dear DR. David Case,
Thanks for the reply..
I downdloaded the file called bugfix(1).all and added to amber10 directory.. (i alreday have a file named containing bugfixes 1to7)..i am thinking to rename the file bugfix(1).all as bugfix.all...and to run the command as:

patch -p0 -N -r patch_rejects <bugfix.all ....(or with the name bugfix(1).all as patch -p0 -N -r patch_rejects <bugfix.all)...

 if i need to do only bugfix21 then....should i copy the whole file to

   amber10/src/mm_pbsa/molsurf.c and run as:

patch -p0 <bugfix.21?

From: David A. Case <>
To: AMBER Mailing List <>
Sent: Tuesday, 2 June, 2009 7:35:09 PM
Subject: Re: [AMBER] Error in MM PBSA

On Tue, Jun 02, 2009, Vikas Sharma wrote:

> molsurf: molsurf.c:1055: is_buried: Assertion
> `sarg1 >= 0.0' failed.


(You could get this by searchig for "is_buried" at the Amber mailing list
archive.) This is also now posted as bugfix.21 at


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