PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2 Commands used: http://pastebin.com/raw.php?i=YYG5ad7A Compressed folder containing all files (10.2 MB): http://www.sendspace.com/file/rka8ei
So I want to simulate this complex. I am having problems with the .itp's and do not know why. I get the error: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/topio.c, line: 656 Fatal error: Syntax error - File NAG_GMX.itp, line 3 Last line read: '[ atomtypes ]' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here is the logic I used while trying to get teh simulation to work, please let me know if this is correct, because there wasn't a tutorial example like this. 1.) Separate the complexed pdb into teh standard residues and ligands, so "ATOM", "HEM", "NAG" and "S58"in this case. 2.) There are multiple ligands in the pdb, so I need to delete all but one molecule and create a forcefield .itp so I can include it in the .top file. 3.) Once the .itp's for the single molecules are created, you need to put the complex back together. I was having problems with adding charges, so I only added hydrogen’s to the ligands and created complex.pdb from the new pdb files created from acpype. 4.) Minimize, relax waters, then simulate. So what did I do wrong here? Thanks!! :) -- 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
