AMBER Archive (2002)

Subject: Protonate doesn-t recognize by pdb input file

From: David Case (case_at_scripps.edu)
Date: Wed May 22 2002 - 11:20:20 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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