[gmx-users] HIS as HID or HIE

[Justin Lemkul]

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

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

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