AMBER Archive (2002)

Subject: SHAKE...

From: Arvid Soederhaell (arvid_at_fmp-berlin.de)
Date: Mon Jun 24 2002 - 06:25:05 CDT

Thaks for the comments on my SHAKE problems!

I'm now going through the OFF files describing the lipids again, and i
have noticed that when loading a pdb file (containing the membrane) into
xleap i get a funny message:

+---Tried to superimpose torsions for: *-C9-O5-*
+--- With Sp2 - Sp0
+---Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported

And when i read in the manual on "addAtomTypes" it says that one can get
funny mssages about the hybridization if the atom types are not defined.
Hence, i went to the OFF file and took a look again. The atom types seems
to be perfectly defined, at least as far as i can see. Is the message
about something else, or is it undefined atom types? How to UNAMBIGOUSLY
work out what atom type is really used? If i open the EDIT window in xleap
everything looks OK.

Moreover it would be nice with a description of the fileformat of the OFF
files. Is there such a description available?

Arvid