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

francesco oteri francesco.oteri at gmail.com
Wed May 16 21:13:17 CEST 2012

Dear gromacs users,

I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force

I downloaded the charmm files toppar_carb_apr12.tgz  from
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 *

*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

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

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