Dear gromacs users, I think I solved the problem. I converted armonic angle potentials in the Urey-Bradley potentials using 0 as constant for the 1-3 bond potential.
Is it right in your opinion? Francesco 2012/5/16 francesco oteri <francesco.ot...@gmail.com> > 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 > -- Cordiali saluti, Dr.Oteri Francesco
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