I have a PDB file . I have to remove hydrogen atom from CYS residues. I manually did it and when I'm running pdb2gmx command, it shows error about the hydrogen atoms. I tried -ignh flag but it ends up adding hydrogen to the residue. What should I do ? I need a topology file without hydrogen atoms in the structure file.
I'm not sure if this discussion is already solved by Deepak Raj answer, but manually removing hydrogens from the amino acid mean that the chemical structure of the amino acid did not match the default topology of the forcefield in GROMACS, and assumably generated an error. Using -ignh will automatically add the missing hydrogens to the incorrect amino acid structure.
are you trying to recreate an intermediate state of enzymatic reaction? if so, i don't think gromacs supports it. But, I heard QM-MM support catalytic reactions. Hopefully it solved your problem!
As Jonathan suggested, you can't do that as cystein is parametrized in every force field with all hydrogens that is has in it structure and it doesn't make any sense to do any MM/MD calculations without any of these hydrogen atoms. If you really want/need that (though I have a hard time imagining why) you will have to prepare your own topology for such modified cysteine and get all parameters, e.g. from www.paramchem.org
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