On Jan 11, 2013, at 7:01 AM, Jason Swails wrote:
> 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
>>
I believe the presence of H27 implies the charge should be +1
(protonated nitrogen in an aromatic ring.) If the charge is
really 0, then H27 should be removed.
HTH,
Bud Dodson
>
> 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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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Fri Jan 11 2013 - 06:00:05 PST
