Hi Matthew, On top of the advice of Mark, consider that Copper has a rather peculiar electronic structure, which may make it difficult to model using only a Lennard-Jones potential for the non-bonded interactions. And then it will also matter whether it's Cu(I) or Cu(II). Are you sure that the simple approach you try to take is suitable to give a good enough answer to the issue you want to address?
Cheers, Tsjerk On Mon, Jun 29, 2009 at 1:45 AM, Mark Abraham<mark.abra...@anu.edu.au> wrote: > Matthew Roode wrote: >> >> Greetings all, >> >> Let me preface this by stating I'm new at MD simulation. I am trying to >> perform a simulation which involves non-bonded copper atoms, amongst other >> things. I'm making use of the Lennard-Jones potential to describe the >> non-bonded interactions between them, and I've input the parameters in the >> ff*nb.itp file after ensuring Cu was defined in the ffgmx.atp file. I use >> x2top to generate the topology file, but the program stops on a fatal error >> telling me "No forcefield type for atom Cu (841) with 0 bonds". Can any of >> you out there offer any advice on the cause of said error? Thus far my >> troubleshooting has failed. > > As a general rule, don't use ffgmx. Like it says in the manual and pdb2gmx, > its usage is deprecated. > > What you need is a forcefield that models non-bonded copper. That's easier > said than found. Most forcefields in common use with GROMACS are for > biochemical simulations, so you may not find anything suitable already in > GROMACS. Telling us your whole simulation system would have been a good > idea. Likely, you'll need to search literature for a suitable model, which > GROMACS is likely to be able to implement. That might require a thorough > knowledge of chapter 5 of the manual. > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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