Hi
Gromacs users
I am trying to set a protein-ligand system in gromacs for MD simulation. I took topology and gro file from an external source. Now I combine the gro file of ligand and protein in a combined complex file and do editconf to generate box but Ligands are missing.
Could anybody please suggest me why this is happening and where I am doing wrong?
Thank you in advance.
Sadaf
Hi Sadaf,
it seems you make a mistake when copy the text of your ligand.gro into the receptor.gro. You need to paste your ligand text into receptor.gro, just below the last line of the receptor text and before the box dimensions.
Thankyou, Martiniano Bello for your reply. Actually I had not updated the total number of atoms that's why it did not take ligands.
But I came across another problem:-
By adding ligands parameters in the complex.gro file this way, ligands stay away from protein outside the box rather than in their proper orientation in the binding site. I attached the screenshot. Could you please suggest me how should I solve this problem?
Thank you
Sadaf
It seems the mistake is a result that the ligand conformations used to generate the ligand.gro perhaps did not correspond with that in the complex (ligand coupled close to the protein). You have to check that the ligand conformers used to created ligand.gro correspond with that in the complex (ligands docked to the receptor). I suppose you create the ligand.gro files using PRODRG server?
Hi, Martiniano Bello I initially selected the complex structure in which ligands are in its proper conformation, grep ligands, used topology builder to generate ligands.gro and topology files.
Then I added the ligands.gro into the complex.gro which placed ligands faraway from protein. There are two ligands in the binding site and one at a different place, How should I fix this problem so that ligands should be in their proper place in the binding site?
Thanks
Hi Sadaf,
This mistake can be generated during the minimization step that perhaps used topology builder to create your ligand.gro and your ligands force field (i dont have so much experience using topology builder). A manners to solve this problem, is to skip mimimization, this considering that you ligand conformation submitted to topology wa previusly optimized, in order that program wil not change ligand orientation. Another way is to create your gro and itp files with PRODRG server, skipping the minimization step to avoid changes in ligand orientation.
http://prodrg1.dyndns.org/submit.html
Hi Sadaf Rani ,
You could move the ligand to the binding site in protein by using a command in VMD:
> set sel [atomselect top all] #this to select the ligand
> $sel moveby { 3 0 0) #this is the x y z distance by how ligand will be moved
You can also rotate the ligand in VM if the orientation is off.
Thank you, Martiniano Bello and Rajlaxmi Saha,
Rajlaxmi Saha, I have three ligands among which two are closer to the binding site and one is away, Could you please suggest a bit more How would I know about (x y z) distance exactly will place ligand in proper binding site?
Thanks in advance.
are u copy and pest ligand.pdb file data to bottom part of protein.pdb file after opening them on text editor?
- Badges
- Science topic
- Similar topics
- Filing