User story 1

[amjadkchy]

As a {blank} I want to {blank} so that I can {blank}

As a modeler, I want to convert an atomistic homology model to a CG Martini model so that I can build a system for an CG MD simulation

• atomistic homology model: should be prepped pdb file format (including disulfide bonds)
• convert: workflow exists as pip package (vermouth) to do so
• checks to be done:
  • are there at least 12 disulfide bonds present?
  • are the molecules protonated?
• system can contain N CG protein molecules at a specified concentration (mg/mL), CG water, buffer at specified concentration,
• excipient at specified concentration (e.g. 100 mg/mL protein in 10 mM histidine buffer pH 6, 0.1% w/w PS80, 250 mM sucrose)
• modeler should have to only upload the protein and everything else should be available in a library of common components.
• Should be able to append new components to library

[sgossert]

Need to consider how to CG (or compensate for) any free ions in solution which can come from buffering (pH control) or added salts. Free ions can come from 2 sources: 1. Adding salts to formulation 2. Buffers/charged excipients (histidine(+1)-HCl Arg-HCl)

Ask: Can we CG molecules such as HCl when it disassociates to H+ and Cl-? Would that look like a similar method to CG water (~4 H2O per CG bead) or would we need special considerations? Would we be able to include atomistic ions with the CG beads and maintain simulation stability?

[amburan]

While looking around in the Martini forum we found there is a way to model ions: http://www.cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp Reading into the file it seems they model hydrated ions as a CG bead

[mikemhenry]

Is debye screening modeled in our CG beeds/FF?

[amjadkchy]

Paper showing preferential interactions of different excipients on a mAb surface.

[Cloutier 2020 Trout Molecular computations of preferential interactions of Pro, Arg, NaCl with IgG1 and their impact on aggr and visc.pdf](https://github.com/omsf/OpenPharmMDFlow/files/13823223/Cloutier.2020.Trout.Molecular.computations.of.preferential.interactions.of.Pro.Arg.NaCl.with.IgG1.and.their.impact.on.aggr.and.visc.pdf