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

francesco oteri francesco.oteri at gmail.com
Thu May 17 17:11:33 CEST 2012

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?


2012/5/16 francesco oteri <francesco.oteri at 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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