Re: [AMBER] Ptraj problems

From: Ganesh Krishnan <>
Date: Thu, 11 Mar 2010 10:55:07 -0800 (PST)

It is indeed the same executable.

In fact, I just found out that I don't even have to submit it to LSF to reproduce the error. If I run a shell script on the local node, the same thing happens (pdb files are messed up). Executing the exact same command on the command line works perfectly.

Additionally, ptraj seems to be reading frames that don't exist when run from the shell script. My trajin command is:

trajin 1 40000 100

In some cases my trajectory has less than 40000 frames. When run in shell script mode, it generates snapshots upto 40000 even though those frames don't exist. This problem doesn't occur when run from the command line.

--- On Thu, 3/11/10, Bill Ross <> wrote:

From: Bill Ross <>
Subject: Re: [AMBER] Ptraj problems
Date: Thursday, March 11, 2010, 10:27 AM

> I am trying to generate pdb snapshots using ptraj. I am running
> into a very strange issue. When I try to generate the snapshots
> by submitting a ptraj job to LSF (using bsub), I have very weird
> snapshots (the bonds are messed up). But when I use the exact same
> command and run it on the local node, it works perfectly.

Is it the same executable? If so, it sounds like you are mixing
up your files, maybe because of different path interpretation in
the batch environment. This could still be the case if the executable
is different, but there is an added possibility of a bug in the one
used in the batch env.


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Received on Thu Mar 11 2010 - 11:00:03 PST
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