[gmx-users] mixing Urey-Bradley and armonic in the same rtp file

[francesco oteri]

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
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