AMBER Archive (2008)

Subject: Re: AMBER: problem with traj and strip waters

From: Carlos Simmerling (
Date: Thu Sep 18 2008 - 09:22:30 CDT

did you load the prmtop with no water before loading the trajectory (into
the same molecule)?
traj files don't have # atoms, so you must have picked the wrong thing
somewhere in vmd since it should not have been looking for them.
load the prmtop as amber7 parm, and the traj files as amber coordinates.

On Thu, Sep 18, 2008 at 10:13 AM, Steve Seibold

> Thanks for you comments. So far nothing has worked (i.e. adding "nobox"
> command). I have tried loading both the prmtop and mdcrd into VMD; however,
> I do get an error (in VMD) saying "file.mdcrd could not be loaded because
> the number of atoms could not be determined". I thus, loaded a pdb file of
> my structure containing no waters, but I got the same error message from
> VMD. I would have thought the number of atoms was in the prmtop file? Should
> I remake the topology file again?
> Thanks again for your assistance.
> Steve

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