Hello Ning-- > > For our protein, we are getting eefxpot values of -3457 using v2.39, > but +4999 using v2.51 XPLOR-NIH, with identical scripts and > tables. Do you know the reason for this very large difference in > eefxpot values? > > One of our Apple computers is running v2.39 and another one is > running v2.51, but yielding different structures with different > energies even though the scripts and tables used on these computers > are identical.
There was a major change in the default EEFx parameters between those
versions, as documented in this publication:
Ye Tian, C.D. Schwieters, S.J. Opella, and F.M. Marassi,
``High quality NMR structures: a new force field with
implicit water and membrane solvation for Xplor-NIH,''
J. Biomol. NMR 67, 35-49 (2017) PMID: 28035651, PMC: 5487259.
The attached little script will evaluate the EEFx energy of a given
structure when run as:
/path/to/pyXplor evalEEF.py file.pdb
Note that the invocation of the EEFx term has also changed since the
2.39 version, with the correct invocation present in the script. The
correct invocation is also present in example script shipped with a
given Xplor-NIH version, for instance in
eginput/gb1_rdc/refine_eefx.py
I do not expect that the two versions will give the same energy,
however I do hope that, when initialized correctly, you will get a
comparable or better structures with the newer version.
best regards--
Charles
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
evalEEF.py
Description: Binary data
