[gmx-users] HIS as HID or HIE
jalemkul at vt.edu
Thu Jul 5 14:57:22 CEST 2018
On 7/5/18 8:50 AM, antonia vyrkou wrote:
> 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.
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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