Dear Jac,
you obviously have loaded default force field parameters for RNA/DNA,
e.g. through something like "source like leaprc.ff14SB" which will pull
in all required parameters, again via additional files e.g.
nucleic12.lib. Essentially the charges in your mol2 file in the 9th
field are the charges from the OFF (lib) file you have loaded. So this
looks perfectly fine to me.
Cheers,
Hannes.
On Fri, 20 Mar 2015 16:31:49 +0530
jacob wick <jacobwick.la.gmail.com> wrote:
> 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 - 07:30:02 PDT
