Multiwfn forum

saeed_E

Member

Registered: 2019-12-21

Posts: 237

A very short question regarding "atmdg.pdb" file

Dear Tian,
If possible, please let me ask a very short question.
In the Multiwfn manual, it is stated that the "occupancy" field in"atmdg.pdb" file records the.....
I could not find the word or phrase "occupancy" in the generated "atmdg.pdb" file. So, while there is not such a phrase in the "atmdg.pdb" file, how can VMD read corresponding values?

Sincerely,
Saeed

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: A very short question regarding "atmdg.pdb" file

Dear Saeed,

This is the so-called occupancy data:

After loading atmdg.pdb, you can color atoms according to occupancy property, then the color will display percentage atomic delta-g index

Please note that I updated manual and Multiwfn yesterday, please make sure that you are using latest version of program and reading latest version of manual.

Best regards,

Tian

saeed_E

Member

Registered: 2019-12-21

Posts: 237

Re: A very short question regarding "atmdg.pdb" file

Dear Tian,
Your highly nice and informative comments and presentations are extremely appreciated, my nice friend.
I have downloaded the latest version of Multiwfn; thank you very much.

Please, also , let me state another concern.
In the "atomdg.pdb" file, the value of delta_G_atom is recorded which corresponds to the atomic contribution percentage within any fragment. Theses values, then, can be plotted in a colored manner using "occupancy" option for coloring method, as you nicely described and presented. It seems, instead of atomic delta_G, the values of delta_G_pair to be much more appropriated when we are going to plot colored map since these values include contribution of both atomic fragments which are interacting. Do not you think so?

Sincerely,
Saeed

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: A very short question regarding "atmdg.pdb" file

Dear Tian,
Your highly nice and informative comments and presentations are extremely appreciated, my nice friend.
I have downloaded the latest version of Multiwfn; thank you very much.

Please, also , let me state another concern.
In the "atomdg.pdb" file, the value of delta_G_atom is recorded which corresponds to the atomic contribution percentage within any fragment. Theses values, then, can be plotted in a colored manner using "occupancy" option for coloring method, as you nicely described and presented. It seems, instead of atomic delta_G, the values of delta_G_pair to be much more appropriated when we are going to plot colored map since these values include contribution of both atomic fragments which are interacting. Do not you think so?

Sincerely,
Saeed

I don't well understand your concern about delta_G_pair. delta_G_atom directly reflects atom contribution to interaction between selected two fragments. delta_G_pair is often manually labelled on IGM/IGMH map between corresponding atom pair between two fragments.

saeed_E

Member

Registered: 2019-12-21

Posts: 237

Re: A very short question regarding "atmdg.pdb" file

Dear Tian,

Thank you very much for a prompt reply with nice explanations. Please let me make my meaning more evident taking a simple example into consideration.
Please, suppose the F...N XB interaction in binary complex F(1)-F(2)...N(3)-C(4)-H(5). The IGMH analysis was performed over the optimized complex and the generated "atmdg.txt" includes below values:

Atom delta-g indices of fragment 1 and percentage contributions
Atom 2 : 0.017468 ( 97.05 % )
Atom 1 : 0.000531 ( 2.95 % )

Atom delta-g indices of fragment 2 and percentage contributions
Atom 3 : 0.016134 ( 89.64 % )
Atom 4 : 0.001795 ( 9.97 % )
Atom 5 : 0.000070 ( 0.39 % )

Atom pair delta-g indices and percentage contributions (zero terms are not shown)
2 3 : 0.015670 ( 87.06 % )
2 4 : 0.001729 ( 9.60 % )
1 3 : 0.000464 ( 2.58 % )
2 5 : 0.000069 ( 0.38 % )
1 4 : 0.000066 ( 0.37 % )
1 5 : 0.000001 ( 0.01 % )

Sum of all atom pair dg indices: 0.017999

My interpretations are as follows. Please confirm they are quite correct or please correct my mistakes.

1- Atom F(2) of fragment 1 contributes in the inter-fragmentation by 97.05%. Indeed, in the whole inter interactions between fragments 1 and 2, 97.05 out of 100 should be related to atom F(2) of fragment 1.
2- Atom N(3) of fragment 2 contributes in the inter-fragmentation by 89.64 %. Indeed, in the whole inter interactions between fragments 1 and 2, 89.64 out of 100 should be related to atom N(3) of fragment 2.
3- Inter interaction between atoms F(2) and N(3) constructs 87.06 % of total (whole) mutual interactions between fragments 1 and 2.
4- Since the smallest and largest value of atom delta-g index is 0.39 and 97.05, respectively, we have to adjust values in the "trajectory" menu of VMD between 0.3 and 97.5 to quite properly color different atoms of two fragments. In this way, if the RGB (red....green...blue) coloring scale is selected, those atoms having larger value of atom delta-g index (F2 and N3) should be colored as deep blue.

In advance, many thanks for your kind attention.

Sincerely,
Saeed

Last edited by saeed_E (2021-12-04 16:51:44)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: A very short question regarding "atmdg.pdb" file

Dear Saeed,

Your understanding if fully correct.

However, in the case that atomic contribution varies from 0.39% to 97.0%, I prefer to use 0~100 as color scale, which looks more elegant than using 0.39~97.5.

Best regards,

Tian

saeed_E

Member

Registered: 2019-12-21

Posts: 237

Re: A very short question regarding "atmdg.pdb" file

Dear Tian,
Too many thanks for your highly valuable confirmation; you made me happy.
Since the smallest value is very close to zero and the largest value is very close to 100, once can understand why you select 0-100 as the lower and upper limits.

Sincerely,
Saeed