Some people have pointed out the following: if you examine the leap.log
file after processing a protein, you may see messages like the following:
** Warning: No sp2 improper torsion term for H-H-N3-H
atoms are: H1 H2 N H3
This happens, even thought the leaprc files set the hybridization of atom
type "N3" to "sp3". The problem is that the "non-bonded equivalence"
command in the parm.dat file equivalences not only the Lennard-Jones
parameters, but also the masses and hybridizations. So, N3 (which should
be sp2) ends up getting set to the same hybridization as N (which is sp2).
This is NOT a problem, other than getting a warning like the one above.
LEaP is doing the correct thing (not putting an improper on sp3 nitrogens),
and you can safely ignore the warning. For future releases, we will update
the parm*.dat files to avoid equivalencing sp3 and sp2 atoms.
Thanks to several people who have noted this -- it took me a while to
track down what was going on.
...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Fri Jul 12 2002 - 13:25:35 PDT
