Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command:
trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur compact -center
and selected protein for centering, and system for output.
However, when I load my corresponding gro file to VMD, and then load the xtc file above, the following error occurs:
ERROR) BaseMolecule: attempt to init atoms while structure building in progress!
ERROR) Invalid number of atoms in file: 132259
Info) Using plugin xtc for coordinates from file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
ERROR) Incorrect number of atoms (132259) in
ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc
ERROR) Mismatch between existing molecule or structure file atom count and coordinate or trajectory file atom count.
Info) Finished with coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc.
This is especially strange since I carried out the same procedure several times before. Additionally, I have a parallel system (with an isoenzyme of the enzyme used here, with the same cofactor and the same ligand) and the same steps worked perfectly. As a side note, this happens when I load xtc file without PBC, while does not happen when I load xtc file in the presence of PBC.
Thank you so much in advance!
The number of atoms in your structure file is different from the number of atoms in your noPBC.xtc file
This can happen if the index group you used in the gmx trjconv step did not match the the number of atoms in the original structure file you loaded into VMD. Say, for instance, you had a structure file of a protein surrounded by water and ions with 90000 atoms and that you loaded that structure file into VMD. Then, during the trjconv step you selected an index group of just the protein because you didn't want the waters making the file any bigger. In this case, you would not be able to load that XTC with just the protein (no waters) into the structure file with waters in VMD because they will have a different number of atoms.
So, from what I can tell, you just have to use gmx editconf or gmx trjconv to create a structure file that matches the number of atoms in your noPBC.xtc file. Then VMD should work.
You can use "Chimera" instead of VMD. In "chimera" You can load .xtc file.
JD Tamucci Thank you for your detailed answer. I think it's still strange to come across an inequality between the structure file and the xtc file, since all the steps I've taken so far looks fine. In that case, regardless of the final structure file that was produced after the simulation (gro file), I should create a new gro file by using the commands you mentioned.
JD Tamucci I managed with gmx editconf, thank you so much!
Saumen Saha thank you for your suggestion
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