The Solvate tool has a bug in that if hydrogens are added during the solvation work flow, then all hell breaks loose. If your structure need hydrogens, then what you need to do is use the AddH tool to add them and write the structure to a new PDB file. Using that PDB file you should be able to use the Solvate tool successfully. Let me know if that doesn't work.

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On May 12, 2010, at 11:28 AM, Andrew Tran wrote:

Hi Chimera support,

I am trying to analyze a protein-RNA complex and would like to neutralize the phosphate backbone with ions and solvate the complex. When I try to do this using Chimera (through AMBERtools?), the complex dissociates. Is there a way to add ions and solvate without dissociation of the complex?

Andrew Tran
Brown University
Biochemistry and Molecular Biology
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