[gmx-users] Charmm to Gromacs: Polyols force field

[Justin A. Lemkul]

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 
> automatically.
> 
> 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.

-Justin

> Any suggestion is welcome!
> 
> Muito obrigado!
> eef
> 
> _______________________________________
> 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
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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