[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!!
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