Hi,
I was using chimera (Windows/Linux) and then compiled ambertools (Linux)
directly for preparing a ligand for docking. However, I've run into
problems adding partial charges. Below is a detailed run from the Chimera
log along with a not-so-verbose error message. Any help is appreciated. And
attached is the molecule I'm working with. I've already attached hydrogens
to the attached molecule through 'reduce'.
Thanks!
Paul
==BEGIN ERROR==
Chain-initial residues that are actual N terminii:
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii:
Chain-final residues that are not actual C terminii:
0 hydrogen bonds
Hydrogens added
Charge model: AMBER ff99SB
Assigning partial charges to residue LIG (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/Chimera
1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02,
tight_p_conv=0, scfconv=1.d-10, -i
c:\users\family\appdata\local\temp\tmpk4hkse\ante.in.mol2 -fi mol2 -o
c:\users\family\appdata\local\temp\tmpk4hkse\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2
(LIG)
(LIG)
(LIG) Total number of electrons: 296; net charge: 0
(LIG)
(LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/sqm" -O -i
sqm.in -o sqm.out
(LIG) Error: cannot run ""C:/Program Files/Chimera
1.5.3rc/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c
properly, exit
(LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(LIG)
(LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Failure running ANTECHAMBER for residue LIG
Check reply log for details
--
Paul Rigor
http://www.ics.uci.edu/~prigor
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Received on Mon May 16 2011 - 14:30:02 PDT
