On Fri, Jan 16, 2009, Jenny Iskrenova wrote:
>
> 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)? Other than that, I don't see the problem --
maybe someone else on the list will be able to help.
...dac
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Received on Sun Jan 18 2009 - 01:34:20 PST
