[gmx-users] RNA ffgmx.hdb problems

[Stéphane Téletchéa]

dwunnick at uni-osnabrueck.de a écrit :
> Hello all,
> 
> as a beginner I try gromacs for the first time. At first my aim is just
> the energy minimization of a small RNA aptamer. I started to convert my
> pdb file into a gromacs structure file with pdb2gmx and failed. I obtained
> this error:
> 
> Fatal error: Atom H1* in residue GUA 2 not found in rtp entry with 27
> atoms while sorting atoms. Maybe different protonation state. Remove this
> hydrogen or choose a different protonation state. Option -ignh will ignore
> all hydrogens in the input.
> 
> So I try the -ignh and get another error and some warnings like:
> 
> WARNING: atom H21 is missing in residue GUA 1 in the pdb file. You might
> need to add atom H21 to the hydrogen database of residue GUA in the file
> ff???.hdb (see the manual)
> 
> Fatal error: There were 175 missing atoms in molecule Protein, if you want
> to use this incomplete topology anyhow, use the option -missing
> 
> Cause I use the Gromacs force field which resorts to the file ffgmx.rtp
> and ffgmx.hdb, I check both files. All four nucleotides exist in the
> ffgmx.rtp but no one in the .hdb. So I add the following in-between the
> alphabetical order as suggested in old mails/questions:
> 

1 - avoid using ffgmx since it is deprecated
2 - you should use a more "modern" FF corresponding to your specific RNA 
input (think of amber for instance), and pay attention that atom types 
are correct in your pdb (you'll probably need to correct them if pdb2gmx 
does not recognize and/or assign atom types properly).

Happy hacking :-)

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901