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?
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)
When using AMBER, the first residue should be NGLU, not just GLU. Likewise for
the C-terminus (CXXX). If you name the residue appropriately, the right
hydrogens should be added based on the .hdb entry.
-Justin
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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
-------------------------------------------------------
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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