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 - 04:30:03 PDT
