Dear all,
I think i should make my problem more clearer. When i added only one
hydrogen molecule (which i built up myself with .frcmod and .lib files),
everything is fine and i can save both the .prmtop and .inpcrd files.
However, when i added more than one hydrogen molecules (with TER cards
in-between these hydrogen molecules in .pdb file), and tried to save
parameters, it complained that :
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
and won't let me save the parameters. I know i can simply add these
parameters in the .frcmod file to get rid of this error message, but what i
am thinking is these parameters shouldn't exist as i dont understand for
example why there should be any HD-HD-HD angles.
Best regards,
Rachel
On 11/20/06, Fenghui Fan <fenghui_fan.yahoo.com> wrote:
>
> 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 - 06:07:22 PST
