numbered consecutively References: <[EMAIL PROTECTED]> In-Reply-To: <[EMAIL PROTECTED]> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.7 X-Authenticated-User: densign X-Originating-IP: 171.65.103.75
Regarding addition of ions, apparently resulting in grompp error: Atoms in the .top are not numbered consecutively from 1 > Try this: > > 1. Paste this at the place of my_ions.itp to replace it. > > [ moleculetype ] > NA+ 1 > [ atoms ] > 1 amber99_31 1 NA+ NA+ 1 1 22.99000 > [ moleculetype ] > CL- 1 > [ atoms ] > 1 amber99_30 1 CL- CL- 1 -1 35.45000 > > 2. Replace "Ions 1" with > > Na+ 6 > Cl- 2 Why, yes, that seems to work. How interesting. However, your solution suffers from the problem that it is much simpler and easier to implement than mine. You get an A-. ;) Seriously, though, this is interesting. When I run genion on a system, then afterwards rebuild it with pdb2gmx, it places the ions before the solvent, and places their topologies in topol_B.itp. Further, in topol_B.itp they are listed as one "molecule" with no bonds, and indicated in topol.top as one "molecule." Your solution, on the other hand, makes each ion its own molecule. I like it, but I'm wondering what's going on. Dan Ensign Stanford University _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
