Hi I am new to the Molecular Dynamics field but I have done several docking work before, I have my protein-ligand files and have processed them using the CHARMM GUI Webserver. I have all the folder output, but the problem is I don’t know how to proceed from there on. Like what input should I type (like the starting code) for the HPC Slurm job because i’ve been enountering errors like this:
Program: gmx mdrun, version 2023.4-conda_forge
Source file: src/gromacs/options/options.cpp (line 177)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 14 (out of 16)
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
Hi, usually at the end of the process on the CHARMM-GUI webserver, you can tick your option for which software you are using to run your simulation. From your error, you are using GROMACS thus you should have ticked the GROMACS output. Then, once your charmm-gui file is downloaded, there is inside another folder called ‘gromacs’ where all you need is. You can then read the README and follow along, change the .mdp files if needed etc. Hope this helps !
PS: never forget to source gromacs of course (in case you are a true beginner)
Yes, I have been already able to proceed. I have this README file, I don’t know how to go about with the #Production Code with the While if-else condition, do you happen to know what exact code should I be using?
Hi again,
Usually, you just need to copy/paste the command lines from the README to the terminal. From what I understand from your README, you have to make 1 minimisation, 1 equilibration and then 10 productions. So the While if-else part of the production is there in order for you to launch the 10 production steps one after the other without having to type the same lines again and again. The if-else condition is there to differentiate between the first step of production (which is a starting point) and the 9 others (which are continuations because of the -t flag).
So if you wish to do that kind of production, you just need to copy/paste the entire While block to your terminal.
