[gmx-users] Generating topology for a HEM protein with CHARMM27

zeineb SI CHAIB zeineb-14 at hotmail.com
Thu May 12 16:27:12 CEST 2016

Dear gmx users, 

I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. 

Since my system is complex, I decided to start first with a monomere taking only protein residues and the hem group. 

When I run pdb2gmx, using CHARMM27 FF, I had this error: 
"Fatal error: There were 30 missing atoms in molecule Other_chain_A, if you want to use this incomplete topology anyhow, use the option -missing"! 

I think that this error is about hydrogen atoms but since my PDB is generated by X-RAY diffraction there is no hydrogen! What should I so? 

Thank you in advance for your help.



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