On Fri, 2014-02-28 at 20:43 +0530, Arunima Shilpi wrote:
> Hello Sir
> I am using antechamber to prepare my ligand but there are errors which I am
> not able to debug
>
> My ligand file is ZINC7271.pdb
>
> I used the following command
>
> reduce ZINC7271.pdb > ZINC7271_h.pdb
>
> then
>
> antechamber -i ZINC7271_h.pdb -fi pdb -o ZINC7271.mol2 -fo mol2 -c bcc -s 2
>
> The error is
>
> Error: cannot run "/home/sabnam/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
> bcc() in charge.c properly, exit
>
> and error in sqm.out file is
>
> QMMM: System specified with odd number of electrons ( 195)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.
> how to debug the this error
As far as error messages in Amber go, this one is one of the clearer
ones. Look at your structure using VMD or Pymol or something, and you
will probably see that there are either not enough hydrogens or there is
an extra one that should not be there. Delete the 'extra' ones or make
sure to add the ones that should be there. Blindly trusting a program
to add hydrogens 'correctly' is a bad idea in my opinion. Your chemical
intuition will almost always be better than a program's.
For the error: sqm only supports singlets I believe. Singlet states
MUST have an even number of electrons, but your molecule has an odd
number of electrons. Unless you KNOW you have an open-shell electronic
configuration [1], this indicates that your hydrogens are not correct.
HTH,
Jason
[1] Open-shell systems are rare in biomolecules in my experience. I've
only seen them in transition metals and certain labels used for EPR
studies.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 28 2014 - 08:00:03 PST
