AMBER Archive (2009)

Subject: RE: [AMBER] (no subject)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jan 18 2009 - 12:07:24 CST


> > The only warning that tleap gives is about the net charge of the
> > molecule being non-zero. The structure looks fine in xleap, as well.
> >
> > The bonds look distorted when I load acetate-vac.prmtop and
> > acetate-vac.inpcrd in VMD.
>
> > Would this, really, be a problem with VMD?
>
> Sounds like it. Did you tell VMD you have an "Amber7" prmtop file (not
> just an "Amber" prmtop)?

And did you select "Amber Restart" for the file format of the coordinates?
Inpcrd files are considered to be restart format.

All the best
Ross

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|\oss Walker

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