[gmx-users] Acetonitrile and isopropanol with CHARMM ff

Sonia Milena Aguilera Segura sonia-milena.aguilera-segura at enscm.fr
Wed Jul 5 11:22:59 CEST 2017

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 because acetonitrile is a linear molecule and dihedrals for three colinear atoms this are mathematically 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 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? 

Also, I cannot find an already optimized structure with all hydrogens for isopropanol. Could somenone provide one? 

Thank you very much in advance for your time and help!! 

Best regards, 

Sonia Aguilera 
PhD student 
Montpellier, France 

More information about the gromacs.org_gmx-users mailing list