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i used the trjconv command to save some frames as a separate pdb file. when i load the structure in pymol this is what I get. I am confused is there something wrong with my trajectory?
It’s very difficult for us to say, based on that image. I assume you used the tpr as input when generating the PDBs from the trajectories, right? Otherwise you would lose a lot of information.
I would recommend looking at the PDB files in a text editor and compare them to the PDB specifications. You could also try opening them in other visualization programs to see if they look OK there. Some programs expect certain residue names, they may or may not be the same depending on the force field nomenclature.
thank you. Initially I was using .gro file but once I switched to .tpr file the issue was resolved.