[gmx-users] HIS as HID or HIE

Justin Lemkul jalemkul at vt.edu
Thu Jul 5 14:57:22 CEST 2018

On 7/5/18 8:50 AM, antonia vyrkou wrote:
> Hello,
> I am using GROMACS 5.1.4 and while trying to convert a .pdb file to .gro I
> get the error message
> “Fatal error:
> Atom HD1 in residue HIS 66 was not found in rtp entry HIE with 17 atoms
> while sorting atoms.”
> Is it not possible to treat some HIS molecules as HID  (where HD1 exists)
> and dome as HIE (instead of HD1 there is HE2)?

Choose the protonation state interactively with the -his option of 
pdb2gmx, but note that your structure will have to be stripped of H 
atoms with -ignh if you are changing the protonation state, otherwise 
you'll just end up with the same fatal error.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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