AMBER Archive (2009)

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

From: Ivan Gladich (igladich_at_purdue.edu)
Date: Fri Sep 11 2009 - 15:34:07 CDT

Thank you
  for your useful suggestions and help.
The amoeba.prm that I have attached in the previous mail comes from the
tinker web site.
Indeed, in amoebapro.prm there are not halide and alkali ions
parameters for amoeba force field (that in amoeba.prm are present).
Does already exist a file with these parameters that I can load with
sleap (in the same way of amoebapro.prm) without any problem?

Thanks again

case wrote:
> 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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-- 
-------
Ivan Gladich, Ph.D.

Dreyfus Postdoctoral Fellow
Department of Chemistry
Purdue University
560 Oval Drive, box 140
West Lafayette
IN 47906 USA

Room: 265C
Tel:765-494-5225
e-mail: igladich_at_purdue.edu
web page: http://web.ics.purdue.edu/~igladich/

--------

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