[AMBER] Ptraj problems

From: Ganesh Krishnan <hereisganesh.yahoo.com>
Date: Thu, 11 Mar 2010 09:43:05 -0800 (PST)

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.

My trajectory is an explicit solvent trajectory. I strip the solvent (chloroform) and then generate the snapshots. The input file is shown below:

trajin a.x 1 40000 100

strip :CL*

center :1-84 mass origin
center :1-84 mass origin
image origin center

trajout pdb pdb nobox

When typing the command, I use:
ptraj prmtop < input_file (shown above)

When submitting to LSF, I enter the previous command in a script file and submit it using bsub.

Any comments will be very helpful. Thank you.

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Received on Thu Mar 11 2010 - 10:00:02 PST
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