Multiwfn forum

Dear Lu
What is the reason for;
1- I finished mIGM analysis and trying to get the (Evaluate contribution of atomic pairs and atoms to inter-fragment interaction (atomic and atomic pair delta-g indices as well as IBSIW index))
2- Unfortunately, I couldn't get the same colors deep green for good interactions and blue is for atoms away from interaction.

I did the same as you mentioned;
First, plot color-filled isosurfaces using the IGM_inter.vmd script as mentioned earlier. After that, we need to remove the default representation showing molecular structure, so we enter "Graphics" - "Representation", choose the first term (its current style is CPK), click "Delete Rep" button. Then we drag the previously generated atmdg.pdb into VMD main window to load it. In this file the “occupancy” field records intermolecular interactions, to graphically exhibit its value for every atom, we should let VMD color the atoms according to their occupancy property. We enter "Graphics" - "Representation" again, set "Drawing method" to CPK, and set "Coloring method" to “Occupancy”,
then click "Trajectory" tab, set upper limit of color scale to 50 and press ENTER button, now the system in graphical window should look like below.

Note
Atomic pair delta-g indices and percentage contributions (zero terms are not shown)
    5  351 :   19.556075  (   2.50 % )
    3  351 :   17.894879  (   2.29 % )
  193  350 :   16.489099  (   2.11 % )
  178  350 :   15.737952  (   2.01 % )
   12  350 :   14.503133  (   1.85 % )

check the attached file

Dear Lu

I did not receive your email message, kindly try to resend the articles again.

emails:
melhenawy111@gmail.com
mm.mohammed@nrc.sci.eg

by the way check the following two images and send me your comments.

Thanks

Dear Lian
Here you can find the result of mine, as I understand from reading-out the manual regarding mIGM.
1- From the cluster analysis result I got the selected amino acid residues near the ligand and then save the file in .xyz containing one frame only and upload it to Multiwfn, then follow the steps of mIGM.
The results contain: 1) blue color for strong interactions like H-bond. 2) Green color for the noncovalent interactions like Van der Waals. 3) Red color for allosteric.
Is this result correct and my conclusion right?
Thanks

Dear Lian

One important thing, after I got the selected coordinates for a ligand and the surrounding amino acids in .xyz file for about 1000 frames usinf the following (same residue as within 3.5 of resname LIG  or (not protein and not waters and not ions and not ion)) in VMD, when I used to open .xyz file with notepad++, I got that there are some water molecules and one Ion, so I remove all water molecules and ions from the .xyz file.
So the .xyz file will have only atomic coordinates for amino acids and ligand

Is this, okay? or I should not remove the water molecules?
Kindly, reply for this matter.

Thanks

Dear Dr. Tian Lu
I am greatly appreciating your reply, I would like to inform you that I have succeeded to get the run work. I will attach you the result picture since I got so many red color around my ligand, keeping in mind that I used VMD to choose residues around my ligand within 3.5 A and remove all water molecules and others protein residues and also ions, and grid spacing was 0.13 bohr.
how can I solve this?
By the way, do you think that analyzing IGM (Independent Gradient Model) may get better information than aNCI?
Thanks

I have already added a .pdb file with the same name as .xzy
So, as you mentioned, I have to record correct element names in that .pdb file. so to change CA into carbon 'only'
Note, the .pdb file it too large
Am i right?