[gmx-users] Generating topology for a heme protein

[zeineb SI CHAIB]

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. 

Regards. 


Zeineb