[Chimera-users] Solvate RNA-protein Complex

Eric Pettersen pett at cgl.ucsf.edu
Wed May 12 13:27:34 PDT 2010

Hi Andrew,
	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

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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> Chimera-users at cgl.ucsf.edu
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