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
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@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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rama david