<div><FONT face="comic sans ms"><STRONG>Dear All,</STRONG></FONT></div> <div><FONT face="comic sans ms"><STRONG> </STRONG></FONT></div> <div><FONT face="comic sans ms"><STRONG> I want to calculate the rdf of a particular residue with respect to water, I was able to generate the rdf of the entire protein against the bulk water,but I could not do the same for a particular residue, In the index.ndx file I have specified the groups of that particular residue, but how can I correlate it with the bulk water ? </STRONG></FONT></div> <div><STRONG> <FONT face="comic sans ms">I think I should generate an .ndx file with all the atoms I need as well as the solvent molecules, but I have some basic problem in understanding the preparation of .ndx file, when I am executing the commnad make_ndx and select system, index file is being
prepared, but there I can not specify groups , everytime it is said that group is empty, I am doing some mistake , but can not detcet it, please help in this two matters.</FONT></STRONG></div> <div><FONT face="Times New Roman" size=3></FONT> </div> <div><FONT face="Times New Roman" size=3>regards</FONT></div> <div><FONT face="Times New Roman" size=3>SANGEETA</FONT></div> <div> </div><BR><BR><p> 
        
        
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