I have performed a 100ns simulation of a protein-ligand complex. Now I want to get the final structure of the complex after simulation and superimpose it with the initial structure. What is the process/command to perform this in GROMACS?
Hi Nadim! Depends on what you mean here. If you wish to see the structure as one frame in any visual molecular graphics software then you need to convert your trajectory file and get that one frame (see gmx trjconv routine). If you need to analyze the structure as a secondary structure or see the evolution of dihedrals then you need to run either gromacs routine do dssp or use VMD for that, but make one pdb frame and convert the trajectory as well taking only protein using gromacs. If you want to study contacts between aminoacid residues then you need to use either gmx mdmat or contact maps in VMD.
Dear @Inna, Thank you for your answer. I just want to see the conformational change by superimposing the initial and the last 3D structure file in any graphics software. Will I use gmx trajconv in This case?
Dear Nadim Ferdous, you can extract the first and the last frames by using following commands:
gmx_mpi trjconv -s yourfilename.tpr -f yourfilename.xtc -o 000.pdb -dump 0
gmx_mpi trjconv -s yourfilename.tpr -f yourfilename.xtc -o 100.pdb -dump 100000
Then you can compare the pdb structures with any visualization software.
Taner Erdoğan Stéphane Abel Thanks for sharing these useful commands, I used them and got the final frame of the protein; however the issue is that my protein looks very distorted and sort of stretched and torn, I remember I was doing similar work few years back and got the same output (torn structure) but then there was a set of commands to render the final structure post-simulation and it looked fine. I wonder if I can get guidance over how to fix this distorted structure. Thank you
- Badges
- Science topic