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 =
2.
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?
Regards,
Brian
--
================================ 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
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Jan 06 2014 - 12:30:03 PST
