On Thu, Jan 10, 2013 at 10:15 PM, Changqing Yan <ycqchemical.gmail.com>wrote:
> Dear,
>
> When I want to use antechamber script to transform a molecular in pdb
> format to mol2 format, it returns the error information as:
>
> Running: /usr/local/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 245; net charge: 0
> Number of electrons is odd: 245
> Please check the total charge and your -nc flag
>
Two comments here -- antechamber requires all hydrogen atoms be present in
your input PDB file. Furthermore, antechamber will make no assumptions nor
will it attempt to guess the total molecular charge. Therefore, if you
have a positively or negatively charged moiety, you will need to set the
charge correctly with the -nc flag, as mentioned above.
If all hydrogen atoms are present and you _still_ have an odd number of
electrons, then you clearly have an unpaired electron and will need to use
another QM software to help calculate the charges, since sqm cannot handle
open-shell systems.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jan 11 2013 - 05:30:02 PST
