Dear gromacs users, I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force field.
I downloaded the charmm files toppar_carb_apr12.tgz from http://mackerell.umaryland.edu/CHARMM_ff_params.html and I converted bonded and nonbonded parameters in gromacs format through the script convert_charmm_to_gromacs.pl. I have successfully generated the .top, using pdb2gmx, as well. But when I run grompp, it complains with errors like: *No default Angle types * * * and *No default Improper Dih. types* Look at the attacched file for the complete output from grompp. Now I inspected the missed interaction and, at least for the angle part, I figured out the problem. In the original charm parametrization there are angles parametrized as armonic and other angles parametrized as Urey-Bradley. Moreover, as far as I know, in the rtp file only one form can be used because of the [ bondedtypes ] clause. So my question is: Is there any way to mix, in the same residue (and hopefully in the same .rtp file), angles parametrized in the armonic form and Urey-Bradley parametrized angles? Is a correct solution parametrizing everything as armonic angles and mimic the bond potential between atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value? Francesco
grompp10.log
Description: Binary data
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
