[gmx-users] g_select / Input error or input inconsistency

[Justin A. Lemkul]

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

========================================