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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Received on Mon Sep 14 2009 - 13:38:48 PDT
