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. Sam Samuel Flores Gerstein Lab office: 266 Whitney Ave., Bass 437 New Haven, CT 06520 203.432.5405 Home: 120 Huntington Street New Haven, CT 06511 cell: 203.747.2682 _____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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 Hi 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. Jo -----Original Message----- From: [EMAIL PROTECTED] on behalf of Astrid Maaß Sent: Mon 11/12/2006 10:53 To: [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
