You haven't edited your topology files correctly. If changing the number of ions has not resulting in a change of charge, I'd suggest you haven't added the ions in right; otherwise, I suspect it's something to do with the number of waters. Particularly as the error in coordinates vs. topology is divisible by 3.
----- Original Message ---- From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Thursday, May 8, 2008 11:34:20 AM Subject: [gmx-users] Unable to neutralize my system Dear All When I run the command "genion" specifying the number n type of chrges to be added, it works fine. I also have made changes in my topology file. But somwhow when I run the "grompp" after that it gives me the following error... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 2818600 Excluding 1 bonded neighbours for Na+ 2 NOTE: System has non-zero total charge: -2.399999e+01 processing coordinates... ------------------------------------------------------- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523) does not match topology (ce_myoII_frag0.top, 8461535) ------------------------------------------------------- I tried adding 2 and 3 ions to the system. But it seems to give the same error. Could someone help? Thanks Namitha Mohandas _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
