Protonate doesn-t recognize by pdb input file

From: David Case <>
Date: Wed 22 May 2002 09:20:20 -0700

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:
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            |
Received on Wed May 22 2002 - 09:20:20 PDT
Custom Search