Is there a good way to add crystallographic water to structure used, for example, dowser software, while preparing protein structures for molecular dynamics simulations?
In particular, crystallographic waters should be kept while running MD simulations. Obviously, you can't forget about solvatation of your protein.
I'm not sure if I understood your question right - crystallographic waters are, AFAIK - waters from X-ray structure, orginally found in PDB files.
[edit] Probably you have solvatation on your mind. In order to solvate your system you can use wide spectra of software, the easiest one would be probably solvate plugin in VMD.
You can always write a small code that will add water molecules randomly to your system and then you can check certain parameters like vander waal's distance between H(of H20) and some atom of your protein and this should be greater than a certain value. By this you can choose which water molecules (that you generated) you can keep in the system and which you can remove so that you can avoid overlapping between the water molecules and your protein.
Thanks for your answers, I could be misunderstood. I want to know if I should add crystalographic water to protein structure before its (protein) solvatation?
I'm not sure what do you mean by "add crystalographic water" - they are waters that come from crystal structure while beeing processed in X-ray workflow. So you can't simply add them - they are present in structure :] do you use any PDB file?
If you have any crystal waters in your structure - you should defintely keep them & add solvatation box/droplet or something.
Yes I know that:), but I wonder if adding water molecules to homologous model cavities is appriopriate.
If the waters are meant to be there, sufficient equilibration will allow them to diffuse into those positions. All MD software has built-in methods for solvation, so setting things up is trivial, and it is very easy to test whether the waters enter the hypothesized locations. Personally, I would not make any assumptions about pseudo-crystal positions if the starting structure is not an actual crystal structure.
Materials Studio is an excellent` software for model building. This software might be helpful.
I have this system with crystal waters, but they are not in the binding cavity. After solvation, some water enters the cavity and I want to remove them. Is this correct or water will still enter the cavity during production?
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