ricalessandri / martini3-small-molecules Goto Github PK

E.g., cases of TOLU or PHEN. Not considering the hydrogens of the carbons that are shared leads on average to better bond lengths.

Should be included in a FAQ section or something like that.

When using bartender we need a blank.itp( ex. Enap_blank.itp) file for the input of the "write_bartender_inp.py" file. I am seeing a lot of values set in the blank.itp but doesn't know where they came from. There is no proper instruction on how to generate Enap_blank.itp file efficiently. Also, there is no proper instruction in the bartender repository on this topic. Could anyone please explain to me how to generate the Enap_blank.itp? If we need to do it by hand then can anyone share the tricks to set the values in the blankitp file?

Hi. I try to map the N-DMBI, but I always miss one carbon in the benzene like this

Could you help me mapping N-DMBI correctly?

When chlorobenzene is mapped into a CG model, it is represented as (TC5)2-SX3. The SX3 represents the chlorine atom, the carbon atom on the benzene ring attached to the chlorine, and the two carbon atoms connected to this carbon atom(also are shared with neighboring beads). I'm not sure which carbon atoms on the benzene ring do the other two TC5 represent? Do the other two TC5 represent two carbons and three carbons, respectively, or do they both represent three carbons, including the carbon atom on the opposite position to the chlorine in the benzene ring and are included in the both TC5?

In the parameter file for methyl-benzoate,

; id type resnr residu atom cgnr charge
1 N4a 1 MBZOA O1 1 0
2 TC5 1 MBZOA R2 2 0
3 TC5 1 MBZOA R3 3 0
4 TC5 1 MBZOA R4 4 0

[bonds]
; i j funct length force.c.
1 2 1 0.389 5000 ; cog
1 3 1 0.389 5000 ; cog

Why is there a bond between N4a and two different TC5 atoms?

Wouldn't the structure then look like

       N4a
       /.      \  
  TC5  -  TC5
       \.         /
          TC5

Instead of

     N4a
       |  
  TC5  -  TC5
       \.         /
          TC5

http://cgmartini.nl/images/stories/workshop2021/lectures/second/riccardo/2021-09-02_MartiniWorkshop2021_Small_molecules-vFINAL.pdf

The ones I'm including in the revised manuscript:

• pyrrolidine

I am creating a parameter file for a small molecule, the cg model of this small molecule contains two virtual sites, I set the mass of these two virtual sites to 0, and when generating the tpr file with gmx grompp, I got the error: atom B5 (Res MOL-0) has mass 0 (state A) / 0 (state B), atom B7 (Res MOL-0) has mass 0 (state A) / 0 (state B). If I set all the mass as default values and can normally generate tpr files. What did I do wrong? This is part of my small molecule parameter file.

The piperidine model can be improved. Bead should probably better be SN5. Details coming soon.

Hi, I want to use the Martini3 model to find the binding pocket of the protein. And the molecule is similar with the adenosine. So I am trying to map the adenosine. I read the itp fire for the adenosine from models/martini_v3.0.0_small_molecules_2020PCTSouzaNatCommun.itp and the Supplementary Information for "Protein-ligand binding with the coarse-grained Martini model". I want to know if TN3a and TN5a refer to the two N and one C on the adenine? I know TC6 as the virtual site because that tow rings be modeled with a "hinge" construction, but I'm confused about the TN5a as the virtual site. And the mass of tiny and small beads is 36.79 and 60.05, how to calculate it?

• What is the list of files needed?
  These 8 files.

• What is the minimal validation required?
  Probably logP and density.

It would be good to add a link in the documentation of where to download the exact martini ff file corresponding to the itp file provided here.

1. In the tutorial - both in the repo and at cgmartini.nl - we say:

"Note that the bimodality of the distributions of the first two dihedrals cannot be captured by the CG model."

Which is not true. This should be fixed. Kudos to @paulocts for pointing this out.

Not sure whether this is a bug or a feature, but the mass of a benzene molecule is 108 Da, rather than 78 Da.

In the style of the one in the polyply repo.

• TEMPO: #14
• TMA: PR needed

In the parameter file for caffeine,

[constraints]
#endif
; i j funct length
1 3 1 0.474 1000000 ; cog
1 6 1 0.405 1000000 ; cog
3 6 1 0.599 1000000 ; cog
3 7 1 0.555 1000000 ; cog
6 7 1 0.283 1000000 ; cog

[dihedrals]
; improper
; i j k l funct ref.angle force_k
1 3 6 7 2 180 200

[virtual_sites2]
; sites positioned at 1-a
; site from funct a
5 3 6 1 0.635 ; cog

[virtual_sites3]
; peripheral virtual sites
; site positioned as a linear combination of 3 atoms
; the site is in the same plane
; site from funct a b
2 5 1 3 1 0.640 0.605 ; cog
4 5 3 7 1 0.650 0.600 ; cog

In the [virtual_site2], how do we get the factor 'a'? Is factor 'a' equal to 0.38 (i.e., the distance of bead 3 and bead 5) divided by 0.599 (i.e., the distance of bead 3 and bead 6)? And for the factors 'a' and 'b' in the [virtual_site3], I would very much like to know how to calculate them too.

As agreed on the Martini dev meeting, collection numbering should be removed. Collection files (which can be useful in certain cases) can be kept with _vYYYYMMDD.itp (but probably all the headers of the models contained in the collection should contain the version number).

Only version numbering for the single models should be added, and they should look like the following:

;;;;;; Martini 3 small molecule topology for benzene (BENZ)
;
; Description:
;   Topology with optimized bond lengths.
;
; Reference(s):
;   R Alessandri, et al., Adv. Theory Simul., 2022, DOI: https://doi.org/10.1002/adts.202100391
;   PCT Souza, et al. Nat. Methods, 2021, DOI: https://doi.org/10.1038/s41592-021-01098-3
;
; Category
;       small molecule
;
; Name
;       Benzene
;
; Alias
;       BENZ
;
; Force field
;       martini3001
;
; Version
;       1.0
;

For models of rigid rings, it is common to exclude all the intramolecular non-bonded interactions. However, in N-DMBI, there are not exclude all the intramolecular non-bonded interactions. What are the considerations behind this?

Following 2 lines should have cgnr = 6 and 7, respectively:

• more precise description of how to work with shared atoms in mapping procedures (i.e., using only 1/2 of the contribution in the weights for the bead position.)

Let's collect some more potential FAQ here.

Please post some examples of the parameterization of the small molecules containing charged centers e.g., nitrogen containing heterocycles at physiological pH. or guidelines to treat such centers.

Hi @ricalessandri, is it possible to optimize the new Martini 3 parameters for better modelling the self-assembling of molecules, like surfactants or lipids? I try to parametrize several surfactant models followed the tutorial, but fails to reproduce the aggregating number of micelles.