Re: [PyMOL] problem with amber trajectory

[Dmitry K. <dk...@bi...>]

Sorry Viktor and Warren, but I don't think your suggestions are  
applicable. I have only a single protein molecule in my trajectory,  
which I kept centered at the origin, so it never traverses the  
periodic boundary. I did strip all but 20 waters from it using ptraj  
and created the appropriate topology file for it. That topology and  
trajectory, as I mentioned, work just fine in VMD. And the problem  
begins with the first frame, so its doesn't seem like bounding box  
info is messing it up.

What I thought might be the case is that the format of that ptraj- 
generated topology might be a little different that what PyMOL  
expected, so I decided to try loading the original (fully-solvated)  
topology with the original (fully-solvated) trajectory into PyMOL.  
Well, all it did was tie up my computer for ~15 minutes and then  
crash PyMOL. The trajectory file is pretty large half a Gig) but it  
opens fine in VMD, and doesn't tie up my machine.

I'm sorry to keep harping on the VMD thing - I'd much rather render  
the trajectory in PyMOL because of its obvious graphical superiority,  
but at present I can't do it. Any ideas?
Thanks,
Dmitry



On Nov 20, 2005, at 9:34 PM, Viktor Hornak wrote:

> Dmitry,
>
> is your system a single molecule or is it composed of multiple  
> molecules (e.g. dimer)? Amber should not 'cut' your molecule into  
> pieces, imaging can only separate molecules in a dimer, trimer or  
> such.  Also, was your system solvated? Did you strip water before  
> visualizing in PyMOL? There may be an issue with your trajectory  
> containing box information which might break a correspondence of  
> trajectory coordinates and topology. To test this, see if the first  
> frame of your trajectory looks ok but all others don't. ptraj is a  
> good program to do various manipulations with your trajectory as  
> Warren suggested.
>
> Cheers,
> -Viktor
>
>
> Dmitry Kondrashov wrote:
>
>> Hi,
>>
>> I have a prloblem with viewing AMBER trajectory files,  
>> specifically,  the topology appears messed up. When I load the  
>> trajectory into the  topology object, the structure shows up  
>> dismembered into eight pieces  on the vertices of a cude. I should  
>> note that I can load an AMBER  coordinate file into the same  
>> topology with no problem, and that the  trajectory displays just  
>> fine in VMD.
>> I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in   
>> loading the trajectory, here's the last few lines:
>>
>>  ObjectMolecule: read set 757 into state 757...
>>  ObjectMolecule: read set 758 into state 758...
>>  CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
>>  CmdLoadTraj: 758 total states in the object.
>>
>> I appreciate your help,
>> Dmitry
>>
>>
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