AMBER Archive (2009)

Subject: Re: [AMBER] re: net charge

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Jun 23 2009 - 15:41:24 CDT

Could you send us your input file so that we can figure out what's the
problem?

Best

Junmei

On Tue, Jun 23, 2009 at 2:22 PM, case <case_at_biomaps.rutgers.edu> wrote:

> 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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