AMBER Archive (2006)

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

From: Rachel (comeonsos_at_googlemail.com)
Date: Mon Nov 20 2006 - 06:59:07 CST

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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