[AMBER] Error with cpptraj strip and MMGBSA.py

From: Brian Radak <radak004.umn.edu>
Date: Mon, 6 Jan 2014 15:28:57 -0500

While preparing trajectories for post processing via MM/GBSA, I used the
following procedure:

Using cpptraj:
1) center/image an explicit solvent trajectory
2) strip out the solvent
3) save a "stripped" trajectory

and then one of the following:

Using sander:
1) use imin = 5 for some energy calculations --> This runs without error

Using MMPBSA.py
1) input the stripped prmtop and mdcrd file --> This fails because IFBOX =

I got around this by changing the prmtop by hand (sorry, I no longer have
the output error message from the mdout file), which was pretty simple.

I don't know what, if any, part of this is a bug. Presumably a stripped
trajectory should always have IFBOX = 0? But that doesn't seem strictly
necessary. By the same token, why does MMPBSAY.py require IFBOX = 0 with
igb > 0, if that information is just ignored by sander?


================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
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 radak004.umn.edu                                 :
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Received on Mon Jan 06 2014 - 12:30:03 PST
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