[Chimera-users] About MD movie problem
pett at cgl.ucsf.edu
Wed Jul 30 13:10:47 PDT 2014
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.
UCSF Computer Graphics Lab
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
> 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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