Jack Shultz wrote:
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?
Yep - you may need a well-formatted .hdb file, like the message says :-)
You should check out whether the AMBER port you installed supports this
feature or not. Alternatively, have a look in the file and with a viewer
to see what is present for residue 1 and how the atoms are named, and
whether renaming some atoms will fix the issue.
Mark
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
-------------------------------------------------------
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