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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