Solvating a PDB

1

Hi,

For a piece of coursework on a module I’ve been assigned we have to prepare a grant proposal for an MD simulation on a supercomputer - however I’m a physicist so have been really struggling with the biological elements. For the proposal we have to list how many atoms we are, however we have to solvate our proteins for the simulation, so until I know how many water molecules I need to solvate, I don’t know how many atoms I have in total for the system. I have the PDB files, 1GC1 and 4DVR, from the rcsb.org website, and I am wondering how I can find out how many water molecules I would need to solvate these. I do not need to actually solvate them, I just need to know how many water molecules it would require to do this - if the easiest way to find this out is to solvate them on a piece of software though then I am open to this. I tried to use VMD’s solvate feature, but the .PSF files are not on the rcsb.org website for these proteins, and so I am really struggling.

Any help would be much appreciated.

2

It depends on the size and the shape of the simulation box that will be used.

You can check this great tutorial and use GROMACS to solvate them :

http://www.mdtutorials.com/gmx/lysozyme/index.html

3

How do you find out the size of the simulation box?

4

Also I do not have GROMACS and it seems hard to install?

5

There is a relevant Q & A here:
https://www.researchgate.net/post/How_to_calculate_PBC_box_size_while_doing_protein_unfolding_MD_simulation

GROMACS includes extensive documentation for installation. Since, you just want to estimate a number, you need to do just a standard CPU installation in order to be able to run the commands and create the box/solvate your structures.

However, I strongly suggest you to read at least the tutorial I mentioned, if you will be the one that will perform the simulations. Also, preprocessing steps might be needed to refine the structures before doing the simulation. There are plenty online resources available for GROMACS (e.g. bioexcel has many related videos on youtube) and of course there is literature to check.

7

This was all I could help, sorry. Good luck.