[gmx-users] Md simulation error

maria khan mariabiochemist1 at gmail.com
Thu Oct 27 20:03:36 CEST 2016


Hello dear gromacs users,
i m running md simulation for protein ligand complex that are glutamate
racemase and its inhibitor (KRH) bt it gives an error like "Atom HD1 in
residue HIS 61 was not found in rtp entry HISB with 12 atomswhile sorting
atoms.For a hydrogen, this can be a different protonation state, or itmight
have had a different number in the PDB file and was rebuilt(it might for
instance have been H3, and we only expected H1 & H2).Note that hydrogens
might have been added to the entry for the N-terminus.Remove this hydrogen
or choose a different protonation state to solve it.Option -ignh will
ignore all hydrogens in the input."
where am i doing wrong.
kindly help me out
Regards and thanks.


More information about the gromacs.org_gmx-users mailing list