If the pdb you loaded has standard residue name, the standard template was applied with the charges. You will have to revise those charges in the new template. Make sure to rename your residues in the new template and pdb.
Bill
<div>-------- Original message --------</div><div>From: jacob wick <jacobwick.la.gmail.com> </div><div>Date:03/20/2015 4:01 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] loading molecule in xleap and saving it in mol2 format </div><div>
</div>Dear Hannes,
1 HO5' 18.422427 34.965199 25.873245 HO 1 DC5 0.4422 **** 2 O5' 18.935000
34.195000 25.617000 OH 1 DC5 -0.6318 **** 3 C5' 19.130000 33.921000
24.219000 CI 1 DC5 -0.0069 ****
Here, the 9th column (or field) is having partial charge information,
right? I wonder, I have only loaded my pdb file in the xleap and saved it
in mol2 format. I have not performed gaussian or other thing to add partial
charges but still it is giving me partial charge information. Is it
possible?
Best,
Jac
On Mar 20, 2015 4:08 PM, "Hannes Loeffler" <Hannes.Loeffler.stfc.ac.uk>
wrote:
> On Fri, 20 Mar 2015 11:14:19 +0100
> FyD <fyd.q4md-forcefieldtools.org> wrote:
>
> > > I mean in general, this stars are not there in
> > > the mol2 file but is it ok in my case?
> >
> > Yes - each program adapts the mol2 file format; same 'problem' with
> > the PDB file format...
>
> The four asteriks are place holders for non-optional fields. None of
> the fields leap filled in in this case are, so they are actually
> redundant.
>
> The PDB format is as it is. It just has been much abused for purposes
> it was not originally designed for. If it had only been used as a
> read-only format...
>
>
> > > Moreover, is partial charges are listed in the last column?
> >
> > Yes
>
> No. Charges are the 9th _field_ and are optional. The last and
> 10th, obviously also optional, field are status bits which are probably
> only relevant to Sybyl. The mol2 format is not a column format.
>
>
> Cheers,
> Hannes.
>
>
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Received on Fri Mar 20 2015 - 08:00:03 PDT
