Re: [AMBER] Starting antechamber for preparing ligand molecule

From: David A Case <>
Date: Wed, 18 Mar 2015 09:37:27 -0400

On Tue, Mar 17, 2015, Anasuya Dighe wrote:
> command used : antechamber -i pepstatin_new.pdb -fi pdb -o pepstatin_new.mol2
> -fo mol2 -c bcc -s 2
> Running: /home/amber/amber14/bin/sqm -O -i -o sqm.out
> Error: cannot run "/opt/apps/amber/amber12/bin/sqm -O -i -o sqm.out" of
> bcc() in charge.c properly, exit
> Here is the end of the output file of sqm.out
> --------------------------------------------------------
> QMMM: System specified with odd number of electrons ( 215)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.

To add to what was said before: this issue probably arises because pepstatin
is a charged molecule. The antechamber default is for zero charge, and you
must use the "-nc" flag to change that.


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Received on Wed Mar 18 2015 - 07:00:03 PDT
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