[AMBER] Antechamber trouble with COA-acyl chain

From: Erin Kelly <erkelly4572.gmail.com>
Date: Tue, 12 Jul 2011 09:59:28 -0500

Hello all,

I've been trying to produce a mol2 file from a pdb generated using ChemDraw
because 'reduce' would not add hydrogens to an unrecognized part of my
ligand. The ligand is a COA with a 10 carbon acyl chain. Both COA and the
acyl chain have gone through antechamber with no problems on their own, but
when I put them together the run fails. I notice this because the sqm.out
file populates itself immediately but gets stuck on atom 101. When I cancel
the run I recieve an error message:

*Running: /home/erkelly/amber11/bin/bondtype -j full -i

Running: /home/erkelly/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o

Total number of electrons: 488; net charge: 0

Running: /home/erkelly/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/erkelly/amber11/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit
I've also attached the sqm.out file for reference.

I've tried to save the molecule directly to mol2 from ChemDraw but this
fails in parmchk because it seems to lose all bond information.

Any advice would be greatly appreciated.

Thank you,

Erin Kelly
Iowa State University

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Received on Tue Jul 12 2011 - 08:30:03 PDT
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