make sure you are reading the Amber coordinate file as Amber 7 restart
format, not as Amber coordinates. The Amber coordinates is for trajectory
files.
On Wed, Feb 21, 2018 at 7:17 PM, Stefano Guglielmo <
stefano.guglielmo.unito.it> wrote:
> Dear AMBER users,
> I generated topology and coordinates for a drug-like molecule using
> Ambertools 16; all seems to have gone ok, but as I try to open prmtop and
> prmcrd in VMD the geometry of the molecule is completely altered because
> VMD reads the first number in prmcrd file (i.e. the number of atoms in the
> molecule) as a coordinate: manually deleting the number solves the problem
> of visualization. Is there a workaround different from manually deleting
> the number of atoms in coord file? Or eventually is it possible to delete
> the number without encountering any issues?
> I am using VMD 1.9.3.
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
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>
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Received on Thu Feb 22 2018 - 07:00:05 PST
