[Chimera-users] Fwd: Loading prmtop/mdcrd with partial workout

[Eric Pettersen]

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 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  
>> 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
>>
>>
>>
>>
> ______________________________________________________________________ 
> ______________
>> Be a better friend, newshound, and
>> know-it-all with Yahoo! Mobile.  Try it now.
>> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
>>
>>
>
>
>
>        
> ______________________________________________________________________ 
> ______________
> Be a better friend, newshound, and
> know-it-all with Yahoo! Mobile.  Try it now.  http:// 
> mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080204/cdd0d50c/attachment.html>