On 4/3/13 11:13 AM, Oleksandr Sushko wrote:
Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance criteria.
The output index file contains all the atoms which satisfy the specified
criteria.
For some molecules on the edge only some atoms are within the specified distance
from protein.
So some molecules in the selection are represented only by 1 or 2 atoms out of
3.
Such selection works fine for example for g_hbond, but it does not work for
g_dipoles.
The error in case of g_dipoles is: "index group is not a set of whole molecules"
is there a smart way (except manual editing of .ndx file) to select the whole
molecules within some distance from protein (with COM within specified distance
from protein surface)?
It would help to know exactly what your selection syntax was. I think you can
use something like "same residue as (within ...)" for your selection, but I
haven't tried it.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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