[gmx-users] RNA ffgmx.hdb problems

dwunnick at uni-osnabrueck.de dwunnick at uni-osnabrueck.de
Thu Jun 14 13:43:07 CEST 2007

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:

ADE     3
1       2      H2*       O2*       C2*       C3*
2       3      H61       N6        C6        N1
2       3      H62       N6        C6        N1
GUA     4
1       2      H2*       O2*       C2*       C3*
2       3      H21       N2        C2        N1
2       3      H22       N2        C2        N1
1       1      H1        N1        C6        C2
CYT     3
1       2      H2*       O2*       C2*       C3*
2       3      H41       N4        C4        N3
2       3      H42       N4        C4        N3
URA     2
1       2      H2*       O2*       C2*       C3*
1       1      H3        N3        C2        C4

Afterwards I change the number of aminoacids.dat to 53 and add the
abbreviations. Then I try the command "pdb2gmx -ignh -f Aptamer.pdb" again
and obtained the same error - 175 missing atoms! And all missed atoms are
exactly the atoms I add to the .hdb file.
So, I did something wrong and I have to say, I have no idea what. I
apogolize about this really long Mail. I hope somebody can help me out of

With best and hopefully regards,

Dorith Wunnicke

More information about the gromacs.org_gmx-users mailing list