@@BioinfoCopilot Sir I tried but its not working, Gro file is successfully uploaded but when I load the xtc file on top of that the ChimeraX goes off and it closes itself.
The calculation is done for ligand without having H atoms called non-hydrogen atoms. Heavy atoms is nothing but the ligand without H atoms. Difference is that when you include H atoms your RMSD values go crazy because of H atoms.
I asked poe: I have simulated 100 ns protein-ligand complex by gromacs and i have obtained 10000 frames in trj.xtc file. Please write me gromacs command to obtain 1000 frames in trj.xtc? It's answer: Step 1: Extract 1000 Frames from the Trajectory First, use trjconv to extract 1000 frames from the trj.xtc file: gmx trjconv -s topol.tpr -f trj.xtc -o new_trj.xtc -skip 10 Step 2: Prepare a New Structure File Next, you need to create a new structure file that reflects the state of the system. You can use the last frame of the extracted trajectory. First, extract the last frame to a .gro file: gmx trjconv -s topol.tpr -f new_trj.xtc -o new_structure.gro -dump 100000 Step 3: Generate a New .tpr File Now, use the new structure file to create a new .tpr file with grompp: gmx grompp -f md.mdp -c new_structure.gro -p topol.top -o new_topol.tpr Is poe's suggestion correct?
Yes correct. Check your md.mdp file where you mention your dtsteps. The reason why you get so many frames is due to the dtsteps. Whether it is 1fs or 2fs etc. that you have to check.
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Best tutorial.
Sir, as you talk about interaction energy in this video (at 26:31). Is it protein-ligand binding energy or something else?
Yes it is !
@@BioinfoCopilot Thank for quick reply. Is it ΔG of binding energy?
@GogaRamDCH No thats interaction energy which has no meaning as described in the tutorial of Justin Lemkul.
Sir what is the version of the ChimeraX because in the recent version I'm not able to upload XTC file.
ChimeraX works differently than Chimera. First you have to upload the gro file and then load the xtc file on top of that!
@@BioinfoCopilot Sir I tried but its not working, Gro file is successfully uploaded but when I load the xtc file on top of that the ChimeraX goes off and it closes itself.
Sir please suggest a software for plotting graph other than Xmgrace for xvg files.
You can use Origin or any plotting software even excel to plot. Just convert the xvg file to a readable format.
@@BioinfoCopilot Thank you
IF I want hydrogen bond occupancy percentage for one residue during the simulation what cod should I use,
Thank you.
gmx_hbond analysis
What is the difference between rmsd of ligand with and without h heavy atom ?
The calculation is done for ligand without having H atoms called non-hydrogen atoms. Heavy atoms is nothing but the ligand without H atoms. Difference is that when you include H atoms your RMSD values go crazy because of H atoms.
I asked poe: I have simulated 100 ns protein-ligand complex by gromacs and i have obtained 10000 frames in trj.xtc file. Please write me gromacs command to obtain 1000 frames in trj.xtc?
It's answer:
Step 1: Extract 1000 Frames from the Trajectory
First, use trjconv to extract 1000 frames from the trj.xtc file:
gmx trjconv -s topol.tpr -f trj.xtc -o new_trj.xtc -skip 10
Step 2: Prepare a New Structure File
Next, you need to create a new structure file that reflects the state of the system. You can use the last frame of the extracted trajectory. First, extract the last frame to a .gro file:
gmx trjconv -s topol.tpr -f new_trj.xtc -o new_structure.gro -dump 100000
Step 3: Generate a New .tpr File
Now, use the new structure file to create a new .tpr file with grompp:
gmx grompp -f md.mdp -c new_structure.gro -p topol.top -o new_topol.tpr
Is poe's suggestion correct?
Yes correct. Check your md.mdp file where you mention your dtsteps. The reason why you get so many frames is due to the dtsteps. Whether it is 1fs or 2fs etc. that you have to check.
dt=2 fs. It shoulld be 20fs?