Stéphane Teletchéa wrote that protonate was failing to add hydrogens
to thymine. (Sorry, but I have lost the original message).
First, there is a bug [the second long-dormant bug to have been found
so far today :-( ] See bugfix.13 for Amber 7 on the amber web site.
You can also apply this patch by hand (it's a one-line fix) to amber6
source code as well.
Second, Stef's pdb files were missing the C7 atom for thymine. This could
cause problems down the line -- protonate certainly won't add the methyl
protons if there is no methyl carbon.
Third, Stef said:
"I intended to use this in a script, so I don't want to use xleap for that"
I'll just note that tleap is fine for scripts, and I think is really what
most experienced amber people use more than xleap.
...thanks for the problem report...hope the above helps....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 Wed May 22 2002 - 09:20:20 PDT
