AMBER Archive (2006)

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

From: Rachel (comeonsos_at_googlemail.com)
Date: Mon Nov 20 2006 - 12:42:10 CST

Hi, dear David,

Thanks very much for your reply, I added a space after TER, and it is
working now ;-) thanks again!

Best regards,
Rachel

On 11/20/06, Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
>
> What is the purpose to add this DH? If you want to add
> this DH to a residue, then you should use the PDB file
> of this residue to get the frcmod file, in this way
> you will get what you missed.
>
> Best regards.
>
> Fenghui Fan
>
> --- Rachel <comeonsos_at_googlemail.com> wrote:
>
> > 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_at_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_at_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_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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