Re: [AMBER] Error: cannot run

From: David A Case <>
Date: Thu, 18 Sep 2014 11:00:50 -0400

On Thu, Sep 18, 2014, Vishal Nemaysh wrote:
> i want to prepare the initial topology file for my protein of interest..for
> this i use the command make the mol2 format file ...
> antechamber -i 1YCC_h.pdb -fi pdb -o 1YCC_h.mol2 -fo mol2 -c bcc -s 2
> but the error is appear as i mention i my last mail .....sir as u suggest
> about the sqm.out file ....
> in sqm.out only few lines are appear whih are as follow...
> QMMM: System specified with odd number of electrons ( 2825)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.

Oooh...this is a really large system! Antechamber is designed to help in
parameterization of small organic molecules (or pieces of a larger polymer,
such as amino acid residues). If you are dealing with a "protein of
interest", you probably don't need to run antechamber at all.

The specific problem is that your molecule has an odd number of electrons, but
antechamber is set up to only handle closed shell molecules. It may be that
your molecule has a net charge (in which case, you need to use the "-nc"
flag); but it will need to be a smaller molecule.


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Received on Thu Sep 18 2014 - 09:30:02 PDT
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