From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 21 2004 - 09:58:31 CDT
It sounds like you are trying to load restart files, not 'crd' files.
VMD supports the new restart file format used by Amber 7, but not the
old version of the format. The 'crd' reader in VMD reads trajectory files
only, and does not read the restart files. The organization of the various
Amber file formats is unwieldy for VMD as there's no decent way to detect which
type of file it is a priori. That being said, I do think we can make some
improvements to the way VMD reads the various Amber files, at some expense
in performance. If you're working with Amber 7 files, try loading your
structure using the 'rst7' plugin and let me know if you still have trouble.
On Mon, Jun 21, 2004 at 02:33:11PM +0200, Kamp, Marc vander wrote:
> Dear all / VMD-developers,
> I am using amber-type parameters in namd. I create the AMBER format input files using the tleap-program (which is included in the NAB-distribution available from the Case-group).
> The parmtop file can be read in into VMD without a problem (if you use the parm7 extension the file is automatically recognised) but reading in the crd file as was created by tleap doesn't go well; VMD reads the number of atoms as the first coordinate. This can simply be solved by deleting the first empty line of the crd-file (which makes the number of atoms the first line).
> However, if you want to use the crd file as input coordinates in NAMD (using 'ambercoor'), the first line must be empty again (otherwise the coordinates are not correctly understood, leading to 'infinite' energies in minimization).
> Of course this is not a very urgent problem, but it would be nice if NAMD and VMD would treat crd files equally. As NAMD can directly use the crd-files that are created with AMBER-suite programs, it would in my opinion be best to change the crd-reading possibility in VMD.
> Best to you all,
-- 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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