AMBER Archive (2008)

Subject: Re: AMBER: saveamberparm

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 24 2008 - 09:58:20 CDT

On Wed, Apr 23, 2008, taufik.alsarraj_at_utoronto.ca wrote:

> I was fortunately able to save a silica slap in mol2 format and i can
> load it in xleap and view the structure using edit. However i cannot
> use the command saveamberparm, i get many many errors
>
> for atom .. could not find type ...O.3 or Si
>
> I am using AMBER9
> I used leaprc.ff03ua

The standard amber parameters files, like ff03ua, are for proteins and nucleic
acids. They are not suitable for things like silica. Amber doesn't contain
force field for silica: you will have to construct your own, or get them from
the literature.

...dac

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