[gmx-users] Water permeation through a channel of membrane protein

[Naba]

Dear gromacs users & developers,

I searched about the topic in the subject-line in the mailing list. But I
couldn't find possible solution. I came to know that gmx select can be
effectively used to calculate the number of water molecules within a porin
channel, but I am not getting the clue to do that.

For instance, if my channel is defined by the residues SER65, GLY66, HIS68,
ASN70, VAL73, THR74, MET77, GLN82, ILE83, TYR91 and so on, how to use gmx
select to calculate the upper and lower boundaries and number of water
molecules in side the channel?

Please help.
For reference, here is my gro file:
https://www.dropbox.com/l/scl/AACHT3J_YHEPyPSQRWn2YOmaUNwRY1eRPQw

Regards
Naba



Nabajyoti Goswami

Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India