[gmx-users] Generating topology for a heme protein
zeineb SI CHAIB
zeineb-14 at hotmail.com
Thu May 12 15:37:39 CEST 2016
Dear gmx users,
I'm working on simulating a homodimer with two cofactors (hem and tetrahydrofolat) and its substrate.
My system is complex so I decided to build my topology file step by step; starting with the protein and the heme (and see if it works). I run pdb2gmx, with CHARMM 27 FF on it and I had this error "Fatal error: There were 30 missing atoms in molecule Other_chain_A2, if you want to use this incomplete topology anyhow, use the option -missing".
I don't know what is ' Other_chain_A2'? my PDB file contain 1 chain: chain A; ATOM lines with protein residues and HETATM lines for HEM!!
How should I proceed in my case? Any tutorials.
Thank you in advance for your help.
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