VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jul 15 2008 - 13:21:57 CDT
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- In reply to: L. Michel Espinoza-Fonseca: "problem with correct visualization of residues"
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On Tue, 15 Jul 2008, L. Michel Espinoza-Fonseca wrote:
MEF> Hi all,
MEF>
MEF> In the past few days I've been analyzing MD trajectories generated by
MEF> NAMD. I've been able to load the trajectories and visualize the
MEF> systems without any problem. However, when I write out a DCD-formatted
MEF> trajectory of the protein only and visualize it with the latest
MEF> version of VMD, *all* the N-epsilon-protonated histidines look
MEF> completely distorted. First I thought it could be a problem related to
MEF> my original psf files, but I was able to write out pdb-formatted
MEF> trajectories of the protein alone. Even if I want to write out a dcd
MEF> file from the pdb-formatted trajectory, the problem appears again.
MEF> Thus, I suspect that the problem might be related directed to the
MEF> engine that allows VMD to write dcd files. It is also important to
MEF> mention that I've been testing VMD on different platforms (Linux,
MEF> windows and mac), and I always got the same result.
michel,
where do you get the bonding information for the reduced
.dcd file from? did you write out a matching .psf file?
i have not seen anything like it and i don't see
a reason why it should happen only to one specific
residue type.
cheers,
axel.
MEF>
MEF> All comments will be appreciated.
MEF>
MEF> Cheers,
MEF> Michel
MEF>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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