[Chimera-users] Fwd: Verify integer/non-integer charges in mol2
meng at cgl.ucsf.edu
Mon May 18 09:40:29 PDT 2009
Just thought I would mention that when you use Add Charge (or command
addcharge), it will report in the Reply Log the total charge and also
any residues that have non-integer charges.
On May 17, 2009, at 12:31 AM, Francesco Pietra wrote:
> 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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