Sorry, I digged through the post-list of old user-questions and found the same problem occuring. the answer to the question was written by David v.d.Spoel and was: "the position in the top file where the spc.itp was included is wrong".
In my top file this include statement is at the end of the script. Where should it be ? Thanks Joern ---------- Forwarded Message ---------- Subject: Atom index (1) in settles out of bounds (1-0) Date: Wednesday 07 March 2007 10:53 From: Joern Lenz <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Dear users, I have a question regarding a simulation (using the amber ports) of DNA covalently bound to a protein. First of all I made an entry in the specbond.dat and the bond was correctly build between the a P of the DNA and a Tyr of the protein. After that I started grompp and got the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file ".../bin/x86_64-unknown-linux-gnu/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) the content of the spc.itp file in line 41 is (marked with "==>>": #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OW funct doh dhh ==>> 1 1 0.1 0.16330 Can anyone tell me how to avoid this error and go on with simulations ? Many thanks in advance Joern ------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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