[AMBER] Important Notice Re Sleap (especially with Glycam)

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 14 Mar 2011 10:27:12 -0400

Short version:

1. Users of sleap should update to bugfix 19 of AmberTools 1.4.

2. If you have been using sleap to generate topology files for use
with certain force fields, particularly with GLYCAM, you might need to
re-run your calculations with new input files.

3. We are performing additional validation checks now. Updates will
be posted to this list within a week or so. Users are, of course,
encouraged to perform their own validations. Validating computational
procedures is a highly recommended practice in any case.

More information:

1. Bugfixes 17-19 to sleap made significant improvements in
functionality. In particular, bugfix 19 corrects a bug where negative
force constants associated with dihedral angles were written to the
topology file as positive values. The use of negative values in this
context is valid. Other force fields avoid use of negative numbers by
employing phase shifts.

2. The GLYCAM force fields employ both positive and negative values
for dihedral force constants. Any topology files generated by sleap
for use with GLYCAM are very likely to be incorrect. If you are using
this or any other force field that uses negative numbers anywhere, it
is recommended you check your top files for accuracy (the rdparm
utility can be useful in this). Note that the parameter file contains
other negative numbers that are internal references and are not used
in actual calculations. For more information on parameter and prmtop
file formats, see this URL: http://ambermd.org/formats.html

3. We will be checking prmtop contents directly. We will also check
energies computed by sander and pmemd. To do this properly and
carefully will take a little time. We will post results. Users
wishing to help should contact me off list. Since the implementation
of mixed 1-4 scaling (Amber10 bugfix 26), there is no simple means for
testing. Users of Amber prior to version 10 bugfix 26 can perform a
simple test in the following manner: Build prmtop files for several
relevant and identical systems using both sleap and tleap. It is
critical that the systems be identical, e.g., same number of waters,
ions, etc. Run identical 1-step minimizations for each system using
both prmtops (for each prmtop pair, make sure the starting coordinates
are identical). The energies should be the same.

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Mar 14 2011 - 07:30:04 PDT
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