[AMBER] A few issues

From: Paul, Austin <Austin.Paul.wyss.harvard.edu>
Date: Wed, 13 Feb 2019 14:55:12 +0000


I'm currently in the process of setting up MD with Amber and have hit a few issues that might warrant addressing:
a.) The Amber 2018 Reference Manual makes no mention of the '-s' parameter that must be passed to parmchk2 in order to check against gaff2 atom types.
b.) When using tLEaP to save pdb files, the atom names are not properly aligned. And because atom types are not specified, other programs may interpret Cl-1, for example, as C-l1, treating them as carbons. I see in the change log that this was fixed in cpptraj a couple years ago, but LEaP still has the issue.
c.) When running pdb4amber, the -add-missing-atoms parameter does not work: it appears to be sourcing an old version of the forcefield file. Either the location or the name/capitalization has changed, which should fix the issue.

Let me know if I should provide any more information regarding the above, or should report bugs to different forums.

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Received on Wed Feb 13 2019 - 07:00:03 PST
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