[Chimera-users] About MD movie problem

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 30 13:10:47 PDT 2014


Hi Rama,
	The error you are getting means that residue 4 in chain C of whatever model is at line 17718 of that file (which I'm guessing is the second model if your system has ~8000 atoms) does not exist in the first model of the file.  All models have to have the same residues/atoms.
	But that's not really relevant since reading your system as a PDB file isn't going to save any significant memory vs. reading it as a .tpr/.trr.  If you have 4000 frames of 8000 atoms, thats 32 million coordinates.  Chimera stores coordinates as 3 double-precision [8 byte] floating point values.  So that comes out to roughly 768 MB.  That really shouldn't run you out of memory, but the .trr/.xtc reading code might temporarily use half again as much memory, so a bit over 1GB -- which might run you out of memory if you are only using the 32-bit version of Chimera.  So make sure you are using the 64-bit version.
	The other thing is that recording 4000 frames of a trajectory at 30 frames per second is going to result in a movie that is about two and a quarter minutes long.  Do you really want your movie to be that long?  Perhaps you would want to use the Gromacs trjconv utility (with the "-skip" option) to reduce the number of frames and make this whole process easier.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jul 30, 2014, at 12:00 PM, rama david <ramadavidgroup at gmail.com> wrote:

> Dear Friends,
>       I completed the simulation of peptide ligand and receptor in gromacs. 
> I want to make the simulation movie.  I am using latest version of chimera.
> I also converted the trajectory files into single pdb movie in gromacs.
>  I did following process:
> 
> 1.  Through tool----> Md movie-- 
>      I choose the gromacs option and load the tpr and trr/xtc files.
>       But the software shows that  the memory is not enough. 
>      ( Frame 4000 and atoms 8000)
>  
> 
> 2.  For second time I chose the PDB option for Mdvie. I load the PDB &
>       now I am getting following message : 
>       Residue 4.C not in the first model on line 17718 of Md.pdb file.
> 
>           I am pasting the few lines of md.pdb starting from line 17718 
> 
> ATOM   8852  N   NH2 C   4      61.241  96.447  51.027  1.00  0.00            
> ATOM   8853  H1  NH2 C   4      61.539  97.208  50.457  1.00  0.00            
> ATOM   8854  H2  NH2 C   4      61.923  95.899  51.517  1.00  0.00            
> END
> 
> 
> 
> Could you please help me in the above problem,
> I will be a very thankful to you for your help.
> This is very Important movie for my work.
> 
> I am looking for reply,
> 
> With best Wishes
> Rama David
>      
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