Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01 opls_996 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01 opls_997 C 6 12.01100 0.000 A 3.40000e-01 3.61200e-01
Then in atomname2type.n2t file add the following lines. C opls_995 0 12.011 2 C 0.142 C 0.142 C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 C opls_997 0 12.011 1 C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex <[email protected]> wrote: > I think we've covered this when I was having the same issue. If you're > trying to simulate a multi-molecule system, then just copy the entire > forcefield .ff folder to your local directory and modify the following > files: > > ffbonded.itp > ffnonbonded.itp > atomnames2types.n2t > > No need to create rtp entries for graphene/nanotubes, so you can > ignore that part of Andrea's tutorial. > > Instead of just "C" in his tutorial, come up with a unique label > to avoid conflicts, which should then also be used in your PDB. Then what > I would do is create a topology entry > for just graphene and convert it to a stand-alone itp by stripping off > system > definitions. This is basically opening the top file, removing those > definitions and resaving as *.itp. > > After that, you can just use pdb2gmx on the remaining > parts of the system and complete the system topology by hand. I know, > this sounds like a lot of manual tweaking, but this is the paradigm. > > Good luck! > > Alex > > > MC> I run a graphene nanolayer, usin the below description (from previous > mail. > MC> Now i got an other error. It look like there is a conflict in a force > MC> field system, someone can suggest me how to modify it? > MC> the force field file came from Minoia advices, reported in the web > side! > MC> / > MC> //Program grompp, VERSION 4.6.7// > MC> //Source code file: > MC> /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: > 752// > MC> // > MC> //Fatal error:// > MC> //Syntax error - File forcefield.itp, line 31// > MC> //Last line read:// > MC> //'1 3 yes 0.5 0.5'// > MC> //Found a second defaults directive./* > MC> * > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
