Which program can be used to visualize interaction of protein surface with solvant molecules?

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Annemarie Honegger

What exactly are you trying to do - looking at solvent interactions in a MD trajectory? at solvent molecules visible in X-ray structures? At the degree of solvent exposure by residue orby atom in a structure? Depending on what you want to do, different programs may be optimal to answer your question.

Ghada Osman

hey Annemarie sorry for being unclear

I want to look at solvent interaction in MD trajectory within the distance of 4 A' from my protein surface

In this case I would recommend VMD (Visual Molecular Dynamics) http://www.ks.uiuc.edu/Research/vmd/. In addition to the program itself, there is an extensive script library.

Benjamin Lowe

Yes I would also recommend VMD (Visual Molecular Dynamics), you could use a free plugin such as: http://www.ks.uiuc.edu/Research/vmd/plugins/intersurf/ for surfaces