AMBER Archive (2004)

Subject: AMBER:

From: jwcraft_at_uh.edu
Date: Mon Aug 30 2004 - 14:54:46 CDT

Protonate

I developed the automation script after getting one successful
dyana->leap->sander run completed. It should have worked correctly,
however the same error occurred. FATAL: Atom .R NCYS 1.A HS 14 does not
have a type. I have now discovered that I had correctly modified the
nomenclature for the cysteine residue's proton on the sulfur atom. I
had in fact used HSG as required. That solution was masked because
protonate also changes nomenclature and over wrote my fix. Now I have
added a sed line:

sed -e 's/ HG /CYS/HSG CYS/' < leap_temp.apdb > leap_temp_pro.pdb

after protonate has updated the file and before leap processes the data

Does anyone know how to make protonate produce nomenclature for leap in
the first place. Or at least have tleap recognize the original HG
nomenclature?

My concern is that even though my sed line patches the problem, it
could cause problems in a future protein that has a CYS at some other
location other than the n-terminus. I also know that a serine also
labels a proton HG so global substitution will not work.

To follow the background on this problem, I wrote up a description on
my blog at
http://accesstospace.blogspot.com and included the segment of the PDB
file that applies to the problem.

John Craft
University of Houston

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