[gmx-users] genion question

Samuel C Flores samuel.flores at yale.edu
Mon Dec 11 19:16:46 CET 2006

Hi Guys, 


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.




Samuel Flores

Gerstein Lab


266 Whitney Ave., Bass 437

New Haven, CT 06520




120 Huntington Street

New Haven, CT 06511

cell:    203.747.2682


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.


-----Original Message-----
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

Dear all,

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
commands below:

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 
-0.81310   1.14989
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!

Kind regards,

 Astrid Maaß

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