[Dock-fans] Adding charges to a peptide ligand

Chris Fage cdfage at gmail.com
Thu May 12 14:37:17 PDT 2016


Hello,

I am interested on testing the abilities of dock6 on a 21-residue peptide
ligand. When I use the Add Charge tool in Chimera, I see the error message
below. I am grateful for any suggestions.

Best,
Chris


Model 0 (peptide.pdb) appears to be a protein without secondary structure
assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Charge model: AMBER ff12SB
Assigning partial charges to residue HIS (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/home/chris/.local/UCSF-Chimera64-1.8.1/bin/amber12/bin/antechamber -ek
qm_theory='AM1', -i /tmp/tmpYJ5zHd/ante.in.mol2 -fi mol2 -o
/tmp/tmpYJ5zHd/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
(HIS)

(HIS) Running:
/home/chris/.local/UCSF-Chimera64-1.8.1/bin/amber12/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(HIS)

(HIS) Running:
/home/chris/.local/UCSF-Chimera64-1.8.1/bin/amber12/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(HIS) Total number of electrons: 111; net charge: 1

(HIS) INFO: Number of electrons is odd: 111

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

(HIS)

(HIS) Running: /home/chris/.local/UCSF-Chimera64-1.8.1/bin/amber12/bin/sqm
-O -i sqm.in -o sqm.out

(HIS) Error: cannot run
"/home/chris/.local/UCSF-Chimera64-1.8.1/bin/amber12/bin/sqm -O -i sqm.in
-o sqm.out" of bcc() in charge.c properly, exit

Failure running ANTECHAMBER for residue HIS
Check reply log for details
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