AMBER Archive (2005)

Subject: Re: AMBER: sp0 console message after using addAtomTypes

From: Lorna Stimson (lorna.stimson_at_gmail.com)
Date: Tue Nov 22 2005 - 11:04:07 CST

Hi,

I don't have the > left in my file - i copied it from the log by
mistake - sorry :)

I have tracked down the problem as

 { "OW" "O" "sp3" }

resulting in an error of

atom type OW - unknown hybridization sp3

I will try the file you suggest,

thanks very much for your advice

Lorna

On 22/11/05, David A. Case <case_at_scripps.edu> wrote:
> On Tue, Nov 22, 2005, Lorna Stimson wrote:
> >
> > I saw other people with similar errors who hadnt used the addAtomTypes
> > command, but as the excerpt from my file (below) shows i have done
> > this.
> >
> > >From my xleap command file:
> >
> > > addAtomTypes {
> > > { "HW" "H" "sp3" }
> > > { "OW" "O" "sp3 "}
> > > }
>
> Do you have the "> " characters at the beginning of these lines? That may
> confusing the program. If that doesn't help, you could source
> $AMBERHOME/leap/lib/solvents.cmd (instead of putting the water stuff in your
> file), and see if that has an effect.
>
> ...good luck...dac
>
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