> On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote: > > Dear GROMACS users, > > > > I am currently interested in studying properties of some solvents, among > > them acetonitrile and isopropanol. I would like to use CHARMM force field > > for compatibility with other molecules and I am taking my initial > > structure files from virtualchemistry.org. Does someone know how to run > > the 6-sites model available with the CHARMM ff in gromacs? As I try to run > > the simulation box I get the error "No Defaul Proper Dih. Types". I > > checked the ffbonded file and I didn't see the dihedrals defined as in the > > rtp file. And for what I've understood this is > > Dihedrals aren't required in .rtp files since pdb2gmx generates them.
Dear Justin, Thank you for the comments. Yes, sorry, I was referring to the top file generated by pdb2gmx instead of the rtp file. The top file has the dihedrals defined whereas ffbonded files does not. > > because acetonitrile is a linear molecule and dihedrals for three colinear > atoms > this are mathematically > > There are still H-C-C-N dihedral terms. Yes, they are named in the top file but not really defined in the ffbonded file, which is why I get the error. > > undefined. Also, when I go to check the available itp for acetonitrile in > virtualchemistry.org, I can see that there is a 7-sites model,with a dummy > atom > included. However, for this case, pdb and itp files do not match. I have seen > that this can be sort of solved by fixing the angle as 179.9, but I really > don't > exactly what to change > > or where in the force field files. I have no experience modifying force > > fields. Also, I've seen that for > > Don't modify the force field. The CHARMM parameters for acetonitrile were > generated in CHARMM, which can handle linear angles without the tricks that > GROMACS requires with virtual sites. So, what you are saying is that it is not possible to simulate the 6-sites model of acetonitrile in GROMACS using CHARMM? > > the opls ff both pdb and itp files match, but I really need to use the CHARMM > force field. Are the opls parameters compatible with CHARMM? Any advice? > > > > Don't mix and match force fields. Then, if I cannot run the 6-sites model, what's the advice? I would really need to run acetonitrile with CHARMM, because I have other series of molecules such as cellulose and other saccharides. In that case, what would be the most compatible for field to simulate organic solvents and saccharides? > > > Also, I cannot find an already optimized structure with all hydrogens for > > isopropanol. Could somenone provide one? > > Take any valine side chain and use it. You can generate any missing H easily > with a suitable .hdb entry. > > -Justin Thank you for your advice, Sonia Aguilera PhD student ENSCM -- 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 gmx-users-requ...@gromacs.org.