Re: FW: AMBER: TI - frcmod file

From: Ilyas Yildirim <>
Date: Wed, 13 Jul 2005 16:51:00 -0400 (EDT)

> > I was running into the same problem. Therefore, I created 2 frcmod
> > files. One for the unperturbed state and the other for the perturbed
> > state containing dummy parameters. (I have new atom type in the
> > unperturbed state). This procedure worked ok and I was able to create
> > the .prmtop and the .inpcrd files. The prmtop file contains the force
> > parmeters force constants.

You dont need to create 2 different frcmod file. One is normally enough,
which includes all of the missing parameters.

> > Can't find angle parameter: DH - NB - CK
> > Can't find angle parameter: DH - NB - CB

Did you defined the parameter list for 'DH - NB - CK' and 'DH - NB - CB'
in the frcmod file?

> > ** Warning: No sp2 improper torsion term for NC-CB-CB-N*
> > atoms are: N3 C5 C4 N9
> > ** Warning: No sp2 improper torsion term for NA-C-CB-CB
> > atoms are: N7 C6 C5 C4
> > *** Improper torsion parameters missing ***

Did you defined the improper torsional parameters for these atoms?

> > atom names: H7-C8-N7-C5
> > atom types: H-Cx-NA-CB =pert=> DH-CK-NB-CB
> > Please add a dummy parameter of multiplicity 2
> > for the pert types to your parameter set.
> > - e.g. DH-CK-NB-CB 0.0 0. 2.
> > (This is because multiple torsional potentials may apply to a
> > single torsion, and each is perturbed individually in gibbs.)

This missing one is the one we were talking about. I dont think that this
is going to effect the calculations, because it gives an energy of zero. I
think that it is because AMBER wants the same number of torsional
parameters for the unperturbed and perturbed system.

The rest has the same errors. So, you should define the missing parameters
in your frcmod file. Good luck.


Ilyas Yildirim

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Received on Wed Jul 13 2005 - 22:53:00 PDT
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