>> >> Dean Cuebas wrote: >> Dear users, >> I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex >> >> I¹ve tried to get grompp to work, but I keep getting the following message: >> _______________________________________________________ >> >> creating statusfile for 1 node... >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# >> checking input for internal consistency... >> calling /usr/bin/cpp... >> processing topology... >> Generated 165 of the 1596 non-bonded parameter combinations >> Excluding 3 bonded neighbours for Protein 1 >> Excluding 3 bonded neighbours for IN4 1 >> Excluding 2 bonded neighbours for SOL 8756 >> NOTE: >> System has non-zero total charge: 7.999998e+00 >> >> processing coordinates... >> >> ------------------------------------------------------- >> Program grompp, VERSION 3.3.2 >> Source code file: grompp.c, line: 448 >> >> Fatal error: >> number of coordinates in coordinate file (trp_b4ion.pdb, 28394) >> does not match topology (trp.top, 28402) >> ------------------------------------------------------- >> >> It appears because grompp is ³excluding² the bonded neighbors is what¹s >> making me end up with the different number of coordinates in my coordinate >> and topology files. >> > No, "exclusions" are something else related to the structure of the > force field - atoms connected by bonds shouldn't also be modeled with > non-bonded interactions. The coincidence of 28402-28394=8 equaling 3+3+2 > is just that. > > Rather more significant is that you have a non-zero charge of (rounded) > 8 and you seem to be part way through a process of replacing water > molecules with ions, which usually leaves a system neutral. I'd guess you've > done something wrong there - most likely mislabeled a file. > > Mark
Thanks for your comment, I know realize the issue has nothing to do with "exclusions but I still don't understand the problem I have. I have the same # of molecules in the .top and the .pdf files that are going into grompp: 1 protein, 1 ligand, and 8756 SOL. Everywhere I read, it says that you will get a "warning" noting that the system has a nonzero charge, before you've added any ions. That I understand, and people still generate .tpr files to then use in genion to fix the charges. But, why could the log say I have 8 more sets of coordinates in my .top file than my .pdb file, which causes a fatal error, when I have identical # of molecules???? In fact, I tested my system with the gmxtest suite 3.3.2, and got the following simple error which also claims that a .tpr file can't be made: No topol.tpr file in morse. grompp failed FAILED. Check files in morse 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED (I also reinstalled gromacs and I get the same problem) I've followed the tutorial steps, except that I'm using version 3.3.2 on MacOS X 10.5.6. Any help would be so greatly appreciated. I plan to "update that tutorial for gromacs 3.3.2" and post it back to the gromacs site soon... IF I can get past this point. Dean _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
