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 - 07:57:10 CST

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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