Dear Mo,
We have a work around in the current development tree that writes 2 prmtops,
a charmm force field one and a VMD compatible one. However this has not been
released as a patch for two reasons. The first being that there are already
changes present for explor psf's which changed quite a bit and this patch
needs to be released first. The second is that we are concerned that
somebody might actually attempt to run a simulation with the VMD compatible
prmtop which would be bad.
However, I should mention that you do not actually need the chamber prmtop
for visualizing in vmd. You can simply load your Charmm psf file into VMD
first and then load your amber trajectory file into the molecule that
creates. This will work fine. You can also load a pdb if you choose and use
that. One of the nice things about the way VMD works is that the loading of
molecules and coordinates etc is program independent. So as long as the atom
count and ordering matches you can mix and match AMBER, gromacs, Charmm
topology files and their trajectory / restart files etc.
Good luck,
Ross
> -----Original Message-----
> From: Mo Chen [mailto:mc842.cornell.edu]
> Sent: Wednesday, June 29, 2011 1:20 PM
> To: amber.ambermd.org
> Subject: [AMBER] VMD-Chamber interface
>
> Dear Amber Users/Developers,
> I found VMD could not read in the *.prmtop file that is generated, and
> I
> have noticed in AmberTools tutorial that:
>
> Third party scripts and/or tools which do not correctly parse the
> extensible
> prmtop format
> may have issues with a chamber-generated prmtop file.
>
> So I wonder if there might have been a way to solve this problem?
>
> Best,
> Mo Chen
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Received on Thu Jun 30 2011 - 02:30:03 PDT
