I've been able to set up everything correctly according to the tutorial I found on the website. I got the following error when I typed: grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr
Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file 1qlz.top, line 7226]: System has non-zero total charge: -2.999999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. processing coordinates... ------------------------------------------------------- Program grompp, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (1qlz-solvated.pdb, 24574) does not match topology (1qlz.top, 24672) I'm stuck. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
