AMBER Archive (2009)

Subject: [AMBER] water bonding with protein

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue Apr 14 2009 - 21:55:39 CDT

Hi, I have a protein that I am running MD on, and it comes with 300 water molecules in the pdb. After I generate a prmtop file, I open my pdb file in VMD, and it says that there are unnatural bonds between the water and the protein. Is this just because the waters are close to the protein in the pdb file? Or when I generated the prmtop file, did it parameterize my system with these unnatural bonds? I mean, when I run the MD with my prmtop file, will it run as if the waters are bound to the protein? Should I worry about this?
Thank you very much for your consistently excellent help.
Mark
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