AMBER Archive (2008)

Subject: AMBER: Sander instead of PMEMD

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Fri May 30 2008 - 08:47:13 CDT

Dear Ambers,

I have a problem running PMEMD on our cluster. As far as I understand it
does not seem to be a program problem but rather the way that our
cluster is build (on module, environments, etc.). I want to do some
MMPBSA calculations on a protein-peptide ligand complex. Can I use for
the production run, Sander instead of the PMEMD? With the periodic
boundary condition parameter switched on, and using the same input (.in)
file as for PMEMD?
Would the trajectory obtained in this way be suitable for extracting
snapshots necessary for mmpbsa ?

Thanks,
Cristina

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