Dear All,
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 ?
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.
regards
SANGEETA
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