Hi Francesco, Not 1000% sure I understand your question, but deleting unwanted wanted parts of your structure before playing through a trajectory will in fact save memory for trajectory formats where the coordinates are read only as needed (which is most formats except for PDB -- including Amber format). So bring up your trajectory and without having gone past frame 1, delete the parts you don't want (e.g. "del solvent" -- and whatever command deletes the lipid). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 2, 2008, at 12:22 AM, Francesco Pietra wrote:
What I asked below has no sense. Deleting residues does not freed memory. Of course, because those residues can be resumed. francesco
--- Francesco Pietra <chiendarret@yahoo.com> wrote:
Date: Fri, 1 Feb 2008 12:49:22 -0800 (PST) From: Francesco Pietra <chiendarret@yahoo.com> Subject: Loading prmtop/mdcrd with partial workout To: chimera <chimera-users@cgl.ucsf.edu>
I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box (i.e., unexpected problems of prmtop fitting after that, though I used a prmtop before creating solvent/lipid/box).
Otherwise, I have memory problems with Chimera in loading such an extensive MD (many ns, in various coordinate files) with all the burden of solvent/lipid/box.
My question: is that feasible with Chimera to load a coordinate file, remove solvent and lipid, load a second coordinate file, remove solvent and lipid, and so on for all coordinate files?
Thanks
francesco pietra
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