Dear all,
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.
Zineb.
I replied to your post on gmx-users. I encourage you to continue the discussion there for the sake of continuity.
Dear Justin,
Thank you very much for your answer. I'll continue the discussion on gmx-users.
Best Regards.
Zeineb.
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