[Chimera-users] Failure With DockPrep

Dylan J. Bennett dylan.john.bennett at gmail.com
Tue Jul 10 07:42:33 PDT 2012

Hi, I am attempting to run DockPrep on NQO2 which contains an FAD cofactor.
Everything works until it attempts to add charges to FAD at which point it
returns an error message. If I delete FAD it will return the same error
message for the Zn ion. It seems to be unable to add charges for any
non-amino acid molecules. I am running the latest stable build of Chimera.
Interestingly, I know Chimera used to be able to calculate these charges
with an old version I had but seems no longer able. Below is the reply log.
Thank you.

#0, chain A: nrh dehydrogenase [quinone] 2
#0, chain B: nrh dehydrogenase [quinone] 2
No incomplete side chains
Terminii for WT_noH.pdb (#0) chain A determined from SEQRES records
Terminii for WT_noH.pdb (#0) chain B determined from SEQRES records
Chain-initial residues that are actual N terminii: ALA 1.A, ALA 1.B
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii: GLN 230.A, GLN 230.B
Chain-final residues that are not actual C terminii:
482 hydrogen bonds
Hydrogens added
Charge model: AMBER ff99SB
Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
Assigning partial charges to residue FAD (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/Chimera
1.6.2/bin/amber11/bin\antechamber -ek qm_theory='AM1', -i
c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.in.mol2 -fi mol2 -o
c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2


(FAD) Total number of electrons: 407; net charge: 0

(FAD) INFO: Number of electrons is odd: 407

(FAD)       Please check the total charge (-nc flag) and spin multiplicity
(-m flag)


(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/sqm" -O -i
sqm.in -o sqm.out

(FAD) Error: cannot run ""C:/Program Files/Chimera
1.6.2/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c
properly, exit

(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/bondtype" -j


(FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/atomtype" -i

Failure running ANTECHAMBER for residue FAD
Check reply log for details

-Dylan J. Bennett
 Dylan.John.Bennett at Gmail.com
 (914) 621-1149
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120710/25240f13/attachment.html>

More information about the Chimera-users mailing list