Stas Bobritsky wrote:
After pdb2gmx -f trna.pdb -o trna.gro -v Gromacs says:
WARNING: atom H5'1 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'1 to the hydrogen database of
residue 2MG
in the file ff???.hdb (see the manual)
WARNING: atom H5'2 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'2 to the hydrogen database of
residue 2MG
in the file ff???.hdb (see the manual)
...
...
I try to study hdb file by comparing .rtp, .pdb, and .hdb- entries, but
my PDB structure does not contain any H-atoms.
Where can I read about .hdb entry format for AMBER forcefield?
Chapter five in the manual.
Mark
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