Hi I have the following error when I Add water spc216.gro. [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0)
>From the Archieve, http://www.gromacs.org/pipermail/gmx-users/2007-March/026171.html Quote => "spc.itp includes a [ molecule ] section, all of which must occur before the [ molecules ] section (and you don't want to start a new [ molecule ] before the old one has finished, either!)" 1. "spc.itp includes a [ molecule ] section, all of which must occur before the [ molecules ] section" => did it as the chapter 5, page 103 of tutorial => the error is still there. 2. "you don't want to start a new [ molecule ] before the old one has finished, either! " => how to complete this part? Thank you Lin The page 103 of tutorial, ; The force field files to be included #include "ffgmx.itp" ;Include urea topology #include "spc.itp" [system] Urea in water [molecules] ; molecule name number Urea 1 SOL 1000 Hi Lin, This is also gromacs related, rather than tutorial related. You followed the tutorial and now went off to try the procedures on your own system. As for the question, searching the user list with "settles" and "bounds" gives me the following: http://www.gromacs.org/pipermail/gmx-users/2007-March/026169.html To me that's a rater "exact answer in the Archives of Gromacs". Apparently the spc.itp is included in the wrong place in your topology file. Time to read chapter 5 of the manual and get acquainted with the topology file format. Cheers, Tsjerk ---------- Forwarded message ---------- From: Chih-Ying Lin <[EMAIL PROTECTED]> Date: Thu, Oct 30, 2008 at 7:35 AM Subject: The question from the tutorial: Add water spc216.gro To: Tsjerk Wassenaar <[EMAIL PROTECTED]> Hi I have a molecule, which is not a protein. Then, I made a .top and a .gro file manually. And, I will like to see it in the water. I followed all the procedures I learned from the tutorials. The easiest way for me is to use all the commands and all of the .mdp files from the tutorials. But, I met the problem when I tried to add water into the system genbox -cp 1LW9-PBC.gro -cs spc216.gro -p 1LW9.top -o 1LW9-water.gro It showed : [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I could not find the exact answer in the Archives of Gromacs and it seems that everything is reasonable for me. Would you please instruct me what is the possible error I made? Thank you very much Lin _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
