> > 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
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Mon Jan 19 2009 - 01:11:18 PST
