Thanks in advance.
In order to check the difference between the native structure and the structures obtained from simulations, I need to get the pdb files of the latter to superimpose with the native one.
I got the simulation files md_0_1.edr; md_0_1.gro etc files after running the production step from which I have generated RMSD, energy and density plots using Justin's GROMACS tutorial.
How do I generate pdb files at the particular nano or pico second I desire to compare?
Dear Surakala,
this can easily be done using the GROMACS command
gmx trjconv -s topol.tpr -f md_0_1.xtc -dt 100 -o trj.pdb
(maybe adapt the names of the .tpr and .xtc files). The -dt option causes the command to output a frame (in this case) every 100ps assuming those frames exist in the .xtc file. If you plan to use the pdb file for visualisation, you might want to use the option -pbc mol in addition.
Dear Surakala,
Hi, I beleave you can perfome desired work by using VMD (Visual Molecular Dynamics). You first need to open Gromacs XTC Compressed Trajectory file (.xtc file), leadig to open 100 frames (if 100ns has choosen) in VMD. Next, you need to save trajectory file, after selecting the .xtc then clicking File -> Save Coordinates. Here you can save 0 to 100 frames into pdb files.
I hope it help.
Bests
Dear Surakala,
this can easily be done using the GROMACS command
gmx trjconv -s topol.tpr -f md_0_1.xtc -dt 100 -o trj.pdb
(maybe adapt the names of the .tpr and .xtc files). The -dt option causes the command to output a frame (in this case) every 100ps assuming those frames exist in the .xtc file. If you plan to use the pdb file for visualisation, you might want to use the option -pbc mol in addition.
Use gmx trjconv with -dump option, specify the time in ps at which you want to make pdb or gro.
I guess Peter already mentioned the generalized command.
U can play around using trjconv -h
An additional information. U can use -sep also to make a library of snapshots.
Check the following command.
trjconv -f md.xtc -o _pro.gro -s md.tpr -n index.ndx -sep -center -skip 10
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