leila karami wrote:
Dear Justin
thanks for your attention.
1) my system consists of protein, dna, and water. In my .ndx file,
protein-H is all of non hydrogen atoms of protein and dna. it is my
nomination for .ndx file.
Providing this kind of information up front would have been useful. It's also a
bad idea. If "Protein-H" is actually all non-H protein and DNA atoms, you'll
never achieve what you want. Use Gromacs' default group of Protein-H for what
you want to do. Dealing with a single group of protein and DNA atoms (any
subset) does not allow for the type of selection you need.
2) I want to obtain number of water molecule which are simultaneously
closer than 3 A° from protein and DNA/ /and not protein or dna./
/
I understand your objective. I stand by my previous comments.
-Justin
/
/
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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