CHARMM36 for Protein-Protein calculations

[nikpekbook]

Is it possible to use Charmm36 force field for gmx_mmpbsa calculations in the case for Protein-Protein system. If so, how the index file from the following example should be modified : 

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_protein/

Thank you in advance

[nikpekbook]

P. S. It would be great if you can advice whether the index file for Charmm36 and Charmm27 should be different of not.

суббота, 30 сентября 2023 г. в 23:32:16 UTC+3, nikpekbook:

[marioe911116]

Is it possible to use Charmm36 force field for gmx_mmpbsa calculations in the case for Protein-Protein system.?

Yes

If so, how the index file from the following example should be modified : 

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_protein/?

The index file is independent of the force field you used (is the same regarding the use of charmm36 or 27). The index file should have a group defined for the receptor (contains the atoms belonging to the receptor) and for the ligand (contains the atoms belonging to the ligand)

[nikpekbook]

Thank you very much for your answer. 

And what about input parametr file? I see recommendations for input parameters for Amber and OPLS force fields, but what differences should be done for the following code (I obtained it from the example page for Amber ff) if I run a Protein-Protein calculation in Charmm27:

&general sys_name="Prot-Prot", 

startframe=1, 

endframe=10, 

forcefields="leaprc.protein.ff14SB",

/ 

&gb igb=2, 

=0.150, 

/

Thanks

воскресенье, 1 октября 2023 г. в 00:37:28 UTC+3, marioe911116:

[marioe911116]

when using charmm force field you must provide the topology file with the -cp flag. Thus, forcefields variable is ignored. We and others recommend using PB for charmm. The specific parameters will depend on your system and your research question. 

[nikpekbook]

Thanks a lot. 

воскресенье, 1 октября 2023 г. в 00:54:21 UTC+3, marioe911116: