Thanks Hannes!
On Mar 20, 2015 7:45 PM, "Hannes Loeffler" <Hannes.Loeffler.stfc.ac.uk>
wrote:
> 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 - 07:30:05 PDT
