[gmx-users] Charmm to Gromacs: Polyols force field
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 22 19:46:39 CEST 2010
Eudes Fileti wrote:
> Olá pessoal,
> Recently, McKerrel published his CHARMM force field to polyols (JCTC,
> 2009, 5, 1315).
> I am very interested in using it in GROMACS.
> For this, I began the transfer of the parameters with the following recipe:
> 1) All atom types were added to the atomtypes.atp file;
> 2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
> were added to the ffbonded.itp file;
> 3) van der Waals and Coulomb parameters were inserted properly
> in ffnonbonded.itp;
> 4) The residues were created in a new file named polyols.rtp.
> Well, pdb2gmx works fine! It generates the restraints file (posre.itp),
> configuration file
> (conf.gro) and topology file (topol.itp). But when I run it in grommp,
> the default for
> parameters are not found. Something like:
> ERROR 6 [file topol.top, line 40]:
> No default Bond types
> I know I can insert the parameters by hand in each .top file generated
> by pdb2gmx.
> But what I need to do, so that grompp recognizes the default values
> Did I forgot some file? I'm making some mistake?
Look on line 40 of the topology and see which atoms grompp is complaining about.
You likely forgot to define the parameters for that particular bond type.
> Any suggestion is welcome!
> Muito obrigado!
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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