From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 22 2006 - 15:06:12 CDT
Just FYI, VMD 1.8.4b6 is now VERY out of date. You should be using the
released version of VMD 1.8.4 and not the beta version. (this goes for
everyone else too...)
On Wed, Jun 21, 2006 at 05:55:01PM -0700, Chandra Ramananjara wrote:
> Hi Peter,
> Thanks for your email. The version of VMD that I'm using is VMD for Linux, version 1.8.4b6 (December 22, 2005).
> Thanks, attached to this email is the psf/pdb combo in which the pdb file has the CRYST header, I tried namdenergy on this combo just now and I'm still getting the null results. The pdb file was created using the writepdb command (in VMD) to save the coordinates of a particular frame (frame 78) of the trajectory.
> Yes you're right, if namdenergy is run on a loaded dcd file, it will loop over the trajectory, and the selected atoms of interest (whose interaction energies are to be calcuated) will be updated in each frame. My case is different. In each frame, the atoms of interest (whose interaction energies I want to calculate) are different from frame to frame so its not as straightforward as using just one selection of atoms for all frames. I think the example script I posted in my last email must have confused you, because the atoms of interest were all oxygens. I just did this to simplify the script.
> In the actual script I'm writing, the selection of the atoms of interest (whose interaction energy I want to calculate) is more complicated and the atoms of interest vary from frame to frame so using one selection text (e.g. [atomselect top "name C"]) for all frames in the trajectory is not an option.
> Do you think it might be my version of VMD ? I think the version I'm using (1.8.4b6) is a relatively new version. The pdb/psf combo I'm having problems with are attached to the email. Thanks.
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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