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
--
========================================
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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