-----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of The One And Only Sent: Sunday, 25 August 2013 12:20 PM To: forum Subject: [gmx-users] Ok now what?
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) Check your topology file and make sure that the number of atoms are correct. I guess in your topology you have more water "SOL" atoms than in your pdb file, so check that and amend it accordingly. As you are very new for this work it is obvious that you will face so many error, are you planning to post all those errors every time you get one :) As Justin suggested, better for you to invest time in learning with someone before doing anything. -- 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
