[Chimera-users] Fwd: Loading prmtop/mdcrd with partial workout
pett at cgl.ucsf.edu
Mon Feb 4 11:40:57 PST 2008
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).
UCSF Computer Graphics Lab
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 Pietra <chiendarret at yahoo.com> wrote:
>> Date: Fri, 1 Feb 2008 12:49:22 -0800 (PST)
>> From: Francesco Pietra <chiendarret at yahoo.com>
>> Subject: Loading prmtop/mdcrd with partial workout
>> To: chimera <chimera-users at cgl.ucsf.edu>
>> I am experiencing difficulties with Amber ptraj in removing
>> (i.e., unexpected problems of prmtop fitting after that, though I
>> used a
>> before creating solvent/lipid/box).
>> Otherwise, I have memory problems with Chimera in loading such an
>> (many ns, in various coordinate files) with all the burden of
>> 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,
>> so on for all coordinate files?
>> francesco pietra
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