AMBER Archive (2006)

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

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Mon Nov 20 2006 - 12:10:21 CST

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
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> >
> >
>
____________________________________________________________________________________
> > > > Sponsored Link
> > > >
> > > > $420k for $1,399/mo.
> > > > Think You Pay Too Much For Your Mortgage?
> > > > Find Out! www.LowerMyBills.com/lre
> > > >
> > >
> >
>
-----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to
> > > majordomo_at_scripps.edu
> > > >
> > >
> >
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Do you Yahoo!?
> > Everyone is raving about the all-new Yahoo! Mail
> beta.
> > http://new.mail.yahoo.com
> >
>
-----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> majordomo_at_scripps.edu
> >
>

 
____________________________________________________________________________________
Sponsored Link

Mortgage rates near 39yr lows.
$310k for $999/mo. Calculate new payment!
www.LowerMyBills.com/lre
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu