[gmx-users] 'none' termini fail

Mikko Huhtala mhuhtala at abo.fi
Tue Sep 10 12:47:39 CEST 2002

I was trying to use pdb2gmx to build a topology for a protein with no
termini groups. After choosing terminus type 'None' for both termini I
get following error:

Making bonds...

WARNING: atom H is missing in residue LEU 1 in the pdb file You might
         need to add atom H to the hydrogen database of residue LEU in
         the file ff???.hdb (see the manual)

Fatal error: There were 1 missing atoms in molecule Protein, if you
want to use this incomplete topology anyhow, use the option -missing

I far as I can understand, pdb2gmx is supposed to add hydrogens and
not complain about them missing. Choosing charged or (de)protonated
termini works without errors, as does running pdb2gmx without the -ter
option. This looks like a bug to me. I am using precompiled,
rpm-packaged Gromacs 3.1.4-1 on Linux.


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