Re: [AMBER] ptraj hydrogen bond analysis error

From: Daniel Roe <>
Date: Wed, 17 Mar 2010 18:42:13 -0400

On Wed, Mar 17, 2010 at 5:47 PM, Jamie Romnes <> wrote:

> Hello,
> I'm attempting to get an analysis of side-chain to side-chain hydrogen
> bonding in ptraj from an MD run on a protein of 114 residues. Its
> aborting and I'm guessing due to a memory issue, but I'd like any help to
> see if its something wrong with my input file. Thanks in advance!
> Jamie

Hi Jamie,

This is most certainly a bug in the code somewhere - regardless of your
input you should never get this message. In this case it seems ptraj has
already freed some memory and is trying to do it again. If possible, could
you supply the corresponding topology file and either the trajectory
coordinates, or if that is too big a restart file? This will greatly help in
analyzing your error.



Daniel R. Roe, Ph.D.
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
AMBER mailing list
Received on Wed Mar 17 2010 - 16:00:04 PDT
Custom Search