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I have a system containing protein and water molecules. I am converting into coarse grain but when converting into coarse grain the water molecules are getting removed. I am using the command : python martinize.py -f pept23_wat.pdb -o single-Protein_A.top -x Protein_A-CG.pdb -dssp /usr/bin/dssp -p backbone -ff martini22
Is there any another way instead of just adding it manually or afterwards solvating the system to convert water molecules present in the initial system to into coarse grain with water molecules. If you can provide the command.
I think (but I’m not completely sure) that you would have to re-solvate the protein afterwards. That shouldn’t be very difficult.
Yes, we can resolve the system afterwards but what if we don’t want to resolvate afterwards but the water molecules present in the original structure convert into coarse grain. How should I possibly do that?
By hand, I would guess. Generate a bead at the center of mass of each cluster of four water molecules.
If there are a few crystal water molecules, you could treat those by hand and re-solvate the rest afterwards.
Can you tell me how will the bead be generated at the center of mass of each of four molecules. Is there any command for it.
Not as far as I know. There is no specific command for it in GROMACS at least. It’s possible that there is something available from the Martini developers, but I don’t think so. At least I don’t know of anyone converting all-atom water coordinates to coarse grained. I can see the point if you want to retain a few crystal waters, even if I don’t think they can be treated very well in a coarse-grain representation, since it’s usually only one water molecule or a very specific network of water molecules. So, I’m afraid you’ll have to do it all yourself, perhaps you might have some use for Introduction to MDTraj — MDTraj 1.9.8.dev0 documentation.
Keep in mind, you would have to re-equilibrate the system anyhow.