AMBER Archive (2006)

Subject: Re: AMBER: problems with saving self-built molecules parameters

From: Rachel (comeonsos_at_googlemail.com)
Date: Mon Nov 20 2006 - 08:23:30 CST

Thanks for your reply. Can xleap add H2 molecule (not H atoms)?
Best regards,

Rachel

On 11/20/06, Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
>
> Why you do not ask xleap directly add the H for you?
>
> Best regards.
>
> --- Rachel <comeonsos_at_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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