All, I'm trying to simulate a peptide/water/cosolvent mix in gromacs (3.3.2). I've set up a topology and coordinates and everything seems fine until I run grompp, at which point I get
WARNING 1 [file "solvated.top", line 17]: Overriding atomtype HO WARNING 2 [file "solvated.top", line 22]: Overriding atomtype OH WARNING 3 [file "solvated.top", line 26]: Overriding atomtype H1 Generated 210 of the 210 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 210 of the 210 1-4 parameter combinations Excluding 3 bonded neighbours for solute 1 turning H bonds into constraints... Excluding 1 bonded neighbours for SOL 4816 turning H bonds into constraints... Excluding 3 bonded neighbours for TFE 805 turning H bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 4234 # ANGLES: 11205 # RBDIHS: 10605 # LJ14: 10714 # CONSTR: 2615 # SETTLE: 4816 Walking down the molecule graph to make shake-blocks Double sids (903, 904) for atom 22086 Double sids (903, 904) for atom 22087 Double sids (903, 904) for atom 22088 Double sids (903, 904) for atom 22089 Double sids (903, 904) for atom 22090 Double sids (903, 904) for atom 22091 Double sids (903, 904) for atom 22092 Assertion failed for "n == natoms" in file splitter.c, line 668 dump core ? (y/n):n I've never seen this stuff before. First off, I don't understand the warnings -- what's overriding those atom types? I don't see anything wrong with them or anythign that should override them. Second, what does the business about "Double sids" and "shake blocks" mean? Clearly I've got something wrong in my topology or in the relationship between my topology and gro file, but this is not at all transparent. I'll poke around in the source and see if I can figure out what's going on but I thought I might be able to expedite things by an e-mail to the list. Thanks, David Mobley http://www.dillgroup.ucsf.edu/~dmobley _______________________________________________ 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