loading trajectories with no box line
Is there a way to load trajectories that do not have box lines? I have trajectories from which most solvent and ions have been stripped. They were written with ptraj as amber coordinate files with the "nobox" option. I cannot get these to stay in register for MD movie. I do not have this problem for trajectories for which the box line has not been removed. Mike Bruist Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry & Biochemistry Griffith Hall 147 University of the Sciences in Philadelphia Philadelphia, PA 19104-4495 Phone (Office & Voice Mail): (215) 596-8530 Department Phone: -8839 Department Fax: -8543 E-mail: m.bruist @usp.edu web page: http://tonga.usp.edu/bruist
Hi MIchael, I'm not 100% sure what "stay in register" means, but if it means that molecules are being "wrapped" across box boundaries then you need to use the ptraj "image" command to keep molecules from wrapping across box boundaries (Chimera currently has no ability to do this wrapping on its own). If this isn't what "stay in register" means then please explain further... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 24, 2012, at 1:40 PM, Michael F. Bruist wrote:
Is there a way to load trajectories that do not have box lines? I have trajectories from which most solvent and ions have been stripped. They were written with ptraj as amber coordinate files with the "nobox" option. I cannot get these to stay in register for MD movie. I do not have this problem for trajectories for which the box line has not been removed.
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Michael F. Bruist