[Chimera-users] Fwd: Verify integer/non-integer charges in mol2

Francesco Pietra chiendarret at gmail.com
Sun May 17 00:31:07 PDT 2009

I have found the problems in converting to pdbqr. Please skip this
message to Chimera.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sat, May 16, 2009 at 9:03 PM
Subject: Verify integer/non-integer charges in mol2
To: chimera <chimera-users at cgl.ucsf.edu>

I assigned Amber ff99SB charges to a proven pdb file of standard amino
acids and capping groups (ACE NME), saving as mol2.

Conversion to a pdbqt file with ATD (autodock tool) resulted in
non-integer charge (-5...). Unless something occurred that escaped my
attention, the protein has -5.00000 charge.

My question: how to verify a posteriory the total charge in the
Chimera-written mol2 file, in order to trace back were I have blurred
things? I don't see the total in the mol2 file.

francesco pietra

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