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Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Mon, 13 Oct 2025 12:55:35 +0000

as you see in the last image there are some isosurfaces appeared within the amino acid residues, even though, I put 'Input index of the atoms to define a fragment, e.g. 2,3,7-10' around that for Ligand only.

Kindly, check and comment

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Mon, 13 Oct 2025 12:52:08 +0000

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

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Sun, 12 Oct 2025 17:25:10 +0000

Thanks, Dear Lu
I will check email.
Thanks

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Sun, 12 Oct 2025 15:16:03 +0000

I've sent to mm.mohammed@nrc.sci.eg
The new images look much more reasonable.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Sun, 12 Oct 2025 13:42:15 +0000

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

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Sun, 12 Oct 2025 12:02:25 +0000

I already sent the two articles yesterday. You can directly reply my E-mail to provide your file.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Sun, 12 Oct 2025 09:19:06 +0000

Dear Dr. Lu

Thanks for your reply, How can i send you the file?, send me your email address.

Kindly. send me copy of the recent two articles for mIGM and amIGM. my email address is; melhenawy111@gmail.com

Regards

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Sat, 11 Oct 2025 13:44:14 +0000

The maps look very weird. Perhaps the isovalue was not properly set (should be too small). Without your structure file I cannot reproduce your result and clearly answer this question.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Sat, 11 Oct 2025 07:56:04 +0000

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

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Sat, 11 Oct 2025 03:33:13 +0000

Dear Lian

As you mentioned that NCI is out-of-date and the best is
amIGM is the best method for characterizing dynamically averaged weak interactions. okay
if i will study for a single compound, should I use NCI or mIGM

Thanks, here you are my email address
melhenawy111@gmail.com

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Fri, 10 Oct 2025 09:00:27 +0000

melhenawy111 wrote:

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

If you only want to study interaction between amino acids and ligand, you can remove all other parts.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Fri, 10 Oct 2025 08:58:44 +0000

melhenawy111 wrote:

Dear Tian
Can you share me the above-mentioned manuscripts
Tian Lu, Graphically Revealing Weak Interactions in Dynamic Environments Using amIGM Method, Struct. Bond. (2025) https://doi.org/10.1007/430_2025_95
Tian Lu, Visualization Analysis of Covalent and Noncovalent Interactions in Real Space, Angew. Chem. Int. Ed., 137, e202504895 (2025) DOI: 10.1002/anie.202504895
As i don't have access to get it both.

Please show me your E-mail.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Fri, 10 Oct 2025 08:27:28 +0000

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

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (melhenawy111) — Fri, 10 Oct 2025 07:22:08 +0000

Dear Tian
Can you share me the above-mentioned manuscripts
Tian Lu, Graphically Revealing Weak Interactions in Dynamic Environments Using amIGM Method, Struct. Bond. (2025) https://doi.org/10.1007/430_2025_95
Tian Lu, Visualization Analysis of Covalent and Noncovalent Interactions in Real Space, Angew. Chem. Int. Ed., 137, e202504895 (2025) DOI: 10.1002/anie.202504895
As i don't have access to get it both.

Re: Error: The promolecular density for the element with index of 113 has

dummy@example.com (sobereva) — Fri, 10 Oct 2025 06:13:01 +0000

IGM and aNCI are completely different, the former is used to analyze single frame, while the latter is used to characterize averaged interactions during MD.

aNCI is fully out-of-date. I STRONGLY suggest using the amIGM method proposed by me this year, see:
Tian Lu, Graphically Revealing Weak Interactions in Dynamic Environments Using amIGM Method, Struct. Bond. (2025) https://doi.org/10.1007/430_2025_95

amIGM example has also been provided in the latest version of Multiwfn manual (Section 4.20.13).

amIGM is the best method for characterizing dynamically averaged weak interactions.

In addition, even if you are only interested in studying single-frame, mIGM is also a much better choice than IGM. mIGM was also proposed in the paper mentioned above and can be realized via Multiwfn (see Section 4.20.12 of manual for example).

More information and comparison can be found in my recent review:
Tian Lu, Visualization Analysis of Covalent and Noncovalent Interactions in Real Space, Angew. Chem. Int. Ed., 137, e202504895 (2025) DOI: 10.1002/anie.202504895