AMBER Archive (2002)

Subject: Re: charges-again

From: Cozmuta (ioana_at_wag.caltech.edu)
Date: Wed Aug 07 2002 - 20:47:14 CDT

Hi,

I forgot to mention that I already did check the total charge on my
protein and it is +7 (total charge). I also traced down the fact that this
charge originates from the fact that the 7 terminal ASN residues (the
protein is built of 7 distinct chains) instead of having each a charge of
-1 (because of being terminal the OXT is also present) the charge is zero.
Other than that everything is correct in the structure. So I was wondering
why is amber not able to set the charge to -1 instead of 0 for the
terminal ASN and what's the best way of doing it otherwise.

Thanks in advance for any advice,
Ioana

On Wed, 7 Aug 2002, David A. Case wrote:

> On Tue, Aug 06, 2002, Cozmuta wrote:
> >
> > Leap is warning me that the unperturbed charge of the unit 7 is not
> > zero meaning that my structure bears a charge of +7. However if I load the
> > same file in another program (InsightII) and use the amber ff, the total
> > charge on the structure is zero. I tried to look into the code
> > ($AMBERHOME/src/leap/src/leap/unit.c) but I could not figure out how this
> > charge was obtained and which residues have the charge that does not
> > compensate. I would appreciate any useful hints that would help me
> > understand this.
> >
>
> You can check the charges yourself by using the "edit" option in xleap
> (select what you want, and choose "edit selected atoms"). You can also
> to use the -pqr option in ambpdb to print out the charges. This should help
> you figure out what you have.
>
> ..good luck...dac
>
>