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how to add MGCL2 to my system containing capsid( protein) and DNA ?
- sharifi
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6 months 3 weeks ago #9689
by sharifi
how to add MGCL2 to my system containing capsid( protein) and DNA ? was created by sharifi
I want to add MGCL2 to my system containing proteins and DNA. I am using martini force field2.2. it does not have MG ion.
1) how should I add MG ion to my system when it is not parametrized in martini force field 2.2?
2) can I use CA instead of MG in martini force field 2.2?
3) I am adding 0.001 M of MGCL2, is there any limitation in salt concentration in martini force field 2.2?
4) if I can not use martini force field 2.2, which model can I use? ( the martini force field 3 does not have the MG ion parametrized either)
I am using gromacs.
1) how should I add MG ion to my system when it is not parametrized in martini force field 2.2?
2) can I use CA instead of MG in martini force field 2.2?
3) I am adding 0.001 M of MGCL2, is there any limitation in salt concentration in martini force field 2.2?
4) if I can not use martini force field 2.2, which model can I use? ( the martini force field 3 does not have the MG ion parametrized either)
I am using gromacs.
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- MatsMD
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6 months 3 weeks ago #9690
by MatsMD
Replied by MatsMD on topic how to add MGCL2 to my system containing capsid( protein) and DNA ?
Parameters for divalent ions are very limited in molecular dynamics using standard point charge models. One can probably not observe noticeable differences using standard Ca2+ or Mg2+ models in for instance CHARMM without polarizable models or multiple point models. Especially as in atomistic force fields ions are mostly parametrized against bulk solution properties, and likely not against biological function (see for instance:
pubs.aip.org/aip/jcp/article/154/17/1711...-calcium-force-field
).
Coarse-graining is only going to make this lack of specificity worse, so the exact ion bead is probably not very important. Riccardo gives the suggestion for Martini 3 here: cgmartini.nl/index.php/component/kunena/...glycosylated-protein . For Martini 2 you can use the CA ion as a replacement for MG but that will at best be a poor approximation (CA is larger, different hydration properties).
Coarse-graining is only going to make this lack of specificity worse, so the exact ion bead is probably not very important. Riccardo gives the suggestion for Martini 3 here: cgmartini.nl/index.php/component/kunena/...glycosylated-protein . For Martini 2 you can use the CA ion as a replacement for MG but that will at best be a poor approximation (CA is larger, different hydration properties).
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