AMBER Archive (2009)

Subject: Re: [AMBER] re: net charge

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Jun 23 2009 - 14:22:28 CDT

On Wed, Jun 24, 2009, Vishal Maingi wrote:

> in antechamber (seems to be incorrect to me also) I used input mol2 file
> to make out mol2 file also.its here in this case net charge is -2 with
> error:
>
> antechamber -i new.mol2 -fi mol2 -o main.mol2 -fo mol2 -c bcc
> Total number of electrons: 284; net charge: -2

What is the sum of the charges in the input mol2 file? Since you will be
generating new bcc charges anyway, you may have to zero out the charges in the
input file, especially if they suggest a net charge different than what you
want.

> Running: /opt/amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out

You should look at the mopac.out file to see what error messages might be
there.

>
> but in other case using mol2 input and output as pdb net charge is zero
> also two electrons are less (here I didnt use -nc flag):
>
> antechamber -i new.mol2 -fi mol2 -o abc.pdb -fo pdb -c bcc
> Total number of electrons: 282; net charge: 0

I agree this is weird...suggested fixes are welcome...cc-ing to Junmei.

...dac

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