So what was the problem and how did you solve it? Having the solution here may help someone else down the track who has a similar issue.
Actually I did not solve it yet, but I stopped asking you because I don`t want to disturb you, even why I need to solve it.
If you have any suggestion I will appreciate.
When I give the command: gmx pdb2gmx -f protein.pdb -o protein_processed.gro I see some errors as you will be in the picture attached. I solve these errors be deleting residues that are involved but can these errors during this phase destroying complex.gro file (ligand away from protein).
The error message tells you what to do. Use -ignh. Don’t delete residues. pdb2gmx does not change coordinates, so no, this will not result in the protein and ligand separating. If you start from the docked coordinates and don’t change anything yourself, your coordinates can’t change.
Please see attached all files, I am not able to know where is my mistake. https://drive.google.com/drive/folders/1ol6qYxhnL1mgc907kNok-v9QEXkKYxOS?usp=sharing
Huge file dumps like these are impossible to work with. We’re not familiar with your system, naming conventions, etc. and when I spent time (above) trying to figure out what was going on, I chased down an irrelevant file and it ended up as a waste of time.
I provided a pretty bulletproof protocol above. If you have a docked complex with the ligand positioned appropriately, there’s nothing else to do besides what I’ve suggested. Check your output after everything you do.
I’m going to repeat what I suggested above too, which is what Justin is suggesting too:
This is something that you can problem solve, and find where the problem is introduced, go through your process step by step. At each step visualise the location of the protein and the ligand (ensure check across the PBC too), and also look at the contents of the coordinate file. At which step does the relative location of the protein and ligand change? You’ve noted above that you’ve tried lots of things to solve the issue you are seeing, so you must have pinned down the step where things are going wrong? With what command or process is that occurring?
So, at which step/coordinate files does the “ligand away from protein” first occur?
And if you want people to look at it, you need to make it easy. Large list of files that make sense to you, but to nobody else, isn’t the way.
I prepared correct complex.gro file using Justins recommendation **gmx editconf -f lig.pdb -o lig.gro** the topology for ligand I created as: unk.pdb corrected with Charm-GUI and then converted to mol2file then using perl command I generated fix_mol2file which uploaded to cGenFf to generate str file. I included ligand to topol.top file But now at the step of **gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr** I am having 2 errors which can be by ligand coordinated but dont know why, see attached
I deleted lines for solving ERROR 2 [file unk.prm, line 35]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported. and solving WARNING 4 [file unk.prm, line 20]:
Bondtype U-B was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
The problem now is at the topol file, attached
The atom order mismatch is due to you generating the ligand topology from a .mol2 file with atoms in a different order than your .pdb/.gro coordinates. Again, as we’ve said many times, you need to have consistent files, which you don’t yet.
The parameter problem is one I address weekly on this forum. Please use Google or the search feature of the forum itself.
I solved the problem. Thank you.
Another issue that I need to discuss is if it is necessarily to check and add missing residues of protein before using for MD after docking.
You shouldn’t do anything with incomplete coordinates, unless they are terminal residues, which are often flexible and hard to resolve experimentally.
For doing molecular docking firstly I correct protein including add missing residues and other, but after docking the complex.pdb built from protein.pdbqt and ligand.pdbqt. Should I check for missing residues again after docking.
What makes you think residues will have somehow been deleted? You can easily verify the existence of the modeled residues.
Thank you Dr. Justin.
What is the command to keep MD running even when pc is shut down?
nohup gmx mdrun -deffnm md &