Then you should use antechamber to get the frcmod file
of the HD.For the charge, maybe Gausian will be
needed.I also just learn on frcmod file construction
and I am looking forward to getting your messake.
Best regards.
--- Rachel <comeonsos.googlemail.com> wrote:
> Thanks for your reply. Can xleap add H2 molecule
> (not H atoms)?
> Best regards,
>
> Rachel
>
>
> On 11/20/06, Fenghui Fan <fenghui_fan.yahoo.com>
> wrote:
> >
> > Why you do not ask xleap directly add the H for
> you?
> >
> > Best regards.
> >
> > --- Rachel <comeonsos.googlemail.com> wrote:
> >
> > > Dear amber users,
> > >
> > > I have a problem with saving parameters of the
> > > molecules that I built up
> > > myself. What I need to do is to add some
> hydrogen
> > > molecules into a protein,
> > > and for the hydrogen molecule parameters i
> defined
> > > them myself, as in a
> > > .frcmod file:
> > >
> > >
> >
> >
>
-----------------------------------------------------------------------------------
> > >
> > > # H2 molecule parameters
> > >
> > > MASS
> > > HD 1.008
> > > DH 1.008
> > >
> > > BOND
> > > HD-DH 150.00 0.742
> > > HD-HD 150.0 1.484
> > >
> > > ANGLE
> > > HD-DH-HD 500.0 180.0
> > > HD-HD-DH 0.000 180.0
> > >
> > > DIHEDRAL
> > >
> > > IMPROPER
> > >
> > > NONBON
> > > HD 0.000 0.000
> > > DH 2.920 0.2722
> > >
> >
> >
>
---------------------------------------------------------------------------------
> > >
> > > This is a 3-atom model, where there is a DH atom
> > > in-between two hydrogen
> > > atoms.
> > >
> > > When i added one hydrogen molecule in the
> protein
> > > pdb file and load the pdb
> > > in leap and save the parameters, everything is
> fine.
> > > However, when i tried
> > > to added more than one hydrogen molecules into
> the
> > > protein ( I added TER
> > > card between these hydrogen molecules), it gave
> me
> > > error message:
> > >
> > >
> > > Could not find angle parameter: HD - HD - HD
> > >
> > > ** No torsion terms for HD-HD-DH-HD
> > > ** No torsion terms for HD-HD-HD-HD
> > > ** No torsion terms for HD-HD-HD-DH
> > > ** No torsion terms for DH-HD-HD-DH
> > >
> > > What I am thinking is there shouldn't be any
> > > HD-HD-HD angles, neither any of
> > > those dihedrals it asked for in the hydrogen
> model,
> > > why it asked for them?
> > > how can i correct this error?
> > >
> > > Thanks very much.
> > >
> > > Best regards,
> > >
> > > Rachel
> > >
> >
> >
> >
> >
> >
> >
>
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>
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Received on Wed Nov 22 2006 - 06:07:20 PST
