AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Jan 17 2009 - 20:48:25 CST

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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