here is the pdb file which i use to produce the input file for g09 after
that use this command due to which error come.
antechamber -i name.pdb -fi pdb -o name.com -fo gcrt
On Thu, Sep 21, 2017 at 7:39 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> CAn you please share the coordinates of this molecule?
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> Sent: 21 September 2017 20:04
> To: AMBER Mailing List
> Subject: [AMBER] Antechamber error
>
> I use this command
> antechamber -i name.log -fi gout -o name.prepi -fo prepi \
> -c resp -s 2
>
> this error i face kindly guide
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for Gaussian Output File --
> Status: pass
> -- Check Unusual Elements --
> Status: pass
> -- Check Open Valences --
> Status: pass
> -- Check Geometry --
> for those bonded
> for those not bonded
> Status: pass
> -- Check Weird Bonds --
> Status: pass
> -- Check Number of Units --
> /home/rehan/Downloads/amber16/bin/to_be_dispatched/antechamber: Fatal
> Error!
> This molecule may have more than one unit.
> antechamber can only handle one unit. If the input is a single unit
> then the connectivity is wrong and the geometry may be bad.
> Please convert your molecule to a mol2 file via:
> antechamber -j 5 -at sybyl -dr no
> And then check your molecule with a visualization program;
> manually add missing bonds or delete unwanted bonds as appropriate.
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Received on Thu Sep 21 2017 - 09:30:01 PDT
