AMBER Archive (2009)

Subject: Re: [AMBER] amoeba.prm problem?

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 09 2009 - 14:17:39 CDT

On Tue, Sep 08, 2009, Ivan Gladich wrote:

> I am using sleap and I have used the following line commands
> >source leaprc.amoeba
> >loadoff ions08.lib
>
> and I have loaded the force field from amoeba.prm instead of
> amoebapro.prm because in amoebapro.prm ions like I-, Br- are not defined.

Where did you get the "amoeba.prm" file from? It doesn't look anything
like amoebapro.prm, and clearly has illegal torsions in it.

> read amoeba torsion
> Error: can not get bond for the given two atoms: 26 28

The current (developers?) version has a little better error message:

Error: while creating dihedral 27-26-28-24 central bond does not exist.

But even the message you got is pretty clear: sleap is reading a torsion,
but finds a connection between atom type 26 and atom type 28, for which there
is no corresponding bond term.

In your file, the torsion list and the bond list are inconsistent; this
problem does not occur with amoebapro.prm.

...dac

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