Check the structure you terminal nitrogen attached with carbon has four
valency so it should have charge as +1 that is causing the error.
See this error already mentioned
"Total number of electrons: 211; net charge: 0"
Best
Ashutosh Shandilya
SCFBio, IIT Delhi
On 5 December 2011 16:23, Devlina Chakravarty <devlina.chakravarty.gmail.com
> wrote:
> Hello,
>
> I am trying to run antechamber on a small molecule,
> S-ADENOSYLMETHIONINE, in order to create the parameter files. When I
> tried using the original pdb file, there was a problem with
> connectivity. So I tried using the PRODRG server to create a pdb file
> with Hydrogen added. Now I am facing a different problem. I have
> pasted the error message which I am getting while running antechamber
> below. I have also attached the pdb file I am using and the mopac.out
> file, since there is some problem in finding charges in the mopac.out
> file.
> I would be very obliged if there could be any solution to this issue.
>
> $ antechamber -i SAM-H-prodrg.pdb -fi pdb -o sam.prep -fo prepi -c bcc
>
> Info: Bond types are assigned for valence state 3 with penalty of 1
>
>
>
> Total number of electrons: 211; net charge: 0
> INFO: Number of electrons is odd: 211
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /software/amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out
>
>
> Thanks in advance,
> --
> Devlina Chakravarty
> JRF
> Bose Institute
> Kolkata
>
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Received on Mon Dec 05 2011 - 03:30:02 PST
