AMBER Archive (2007)

Subject: Re: AMBER: Please check the total charge and your -nc flag

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 27 2007 - 16:29:32 CST

On Sun, Mar 25, 2007, snoze pa wrote:
>
> I am trying to convert a pdb file into mol2 file format using antechamber.
> I am using following command
> antechamber -i new_POL.pdb -fi pdb -o new_POL.mol2 -fo mol2 -c bcc -nc
> NET_CHAEGE -m MULTIPLICITY -j 5 -df 0
>
> but it is not working.. Instead I am getting following error message
> Total number of electrons: 255; net charge: 0
> Number of electrons is odd: 255

It looks like you did not put in the net charge on the input line. You
say that you used "-nc NET_CHAEGE", but the argument after the "-nc" flag must
be an integer, not a string. As the program says:

> Please check the total charge and your -nc flag

>
> If i will use
> antechamber -i new_POL.pdb -fi pdb -o new_POL.mol2 -fo mol2 -c bcc -df 0 &
>
> then error message is different like
>
> Warning: the assigned bond types may be wrong, please :

This time you left out the "-j 5" flag. So it makes sense that you will get a
different message. You probably need the "-j" flag for your molecule.

...dac

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