[gmx-users] genion question
Samuel C Flores
samuel.flores at yale.edu
Mon Dec 11 19:16:46 CET 2006
I have a question. I am using genion to add two ZN2+ ions to a protein that
already has two. I thought I would just use genion with np 2. However it
seemed to recognize that there were already two in the file and added none.
So instead I used the parameter np 4. This seemed to add two, for a total
of four, which I wanted. However sometimes it seems to add two too many!
Am I understanding the proper use of the np parameter?
Many thanks in advance.
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From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Hanna, Joanne
Sent: Monday, December 11, 2006 11:02 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] difficulties in creating octahedral boxes
If you do:
editconf -f box.gro -o box.pdb
and view this in rasmol entering the command
set unitcell on
you should see the octahedral box.
To view the octahedral box with the water you need to use the '-ur compact'
option in trjconv.
This should give you the octahedral representation.
From: gmx-users-bounces at gromacs.org on behalf of Astrid Maaß
Sent: Mon 11/12/2006 10:53
To: gmx-users at gromacs.org
Subject: [gmx-users] difficulties in creating octahedral boxes
I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top
When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
line in ex_in_box.gro seems to describe a non cubic box:
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?
I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!
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