I tried to protonate my pdb file using openbabel
babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h
Then I ran pdb2gmx with the following
pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
Protein.top -water spce -ignh
But apparently I am missing a H from my first residue. Is there an
easy way to add missing atoms?
WARNING: atom H is missing in residue GLU 1 in the pdb file
You might need to add atom H to the hydrogen database of residue GLU
in the file ff???.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2top.c, line: 704
Fatal error:
There were 1 missing atoms in molecule Protein, if you want to use
this incomplete topology anyhow, use the option -missing
-------------------------------------------------------
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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