[gmx-users] Protonation state: CYX HID

Kai Zhuang kai.zhuang at gmail.com
Sun Jun 12 03:06:54 CEST 2005


I'm simulating a system that include the HETATM groups: CYX and HID
pdb2gmx seems to have trouble with the protonation state that they are in.

i did:
/usr/local/bin/pdb2gmx -f ZKH-001-001-001.pdb -p ZKH-001-001-001.top
-o ZKH-001-001-001.gro -merge
and got error: 
Fatal error: Atom HB2 in residue CYS 3 not found in rtp entry with 7 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

then i tried with -ignh tag to ignore the hydrogens, got new error:
Warning: 'HID' not found in residue topology database, trying to use 'HIS1'

how should i edit the pdb file?

Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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