Re: protonation of some histidine residues

From: Richard Law (
Date: Fri Sep 14 2007 - 17:08:00 CDT

HSP is not a patch, it's a residue.

Do "alias residue HIS HSP" instead and remove the patch lines.

If you want different histidines to have different protonation states
(which if you've done a pka calculation you will) then you'll need to
change each one rather than doing this "one size fits all" command.

On Fri, 14 Sep 2007 wrote:

> Dear users,
> I've been trying to protonate 3 histidines residues in a protein. I could
> protonate all ASP and GLU residues using "patch" before, but I'm have
> problem with the histidines. The error message that I got is:
> "
> applying patch HSP to 1 residues
> unknown patch type HSP
> "
> Below is the script that I've been using. Please, any help is welcome.
> Thank you very much.
> topology top_all22_prot.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> alias atom GLY OXT OT1
> segment prot { pdb prot_p.pdb }
> coordpdb prot_p.pdb prot
> patch HSP prot:36
> patch HSP prot:81
> patch HSP prot:116
> guesscoord
> writepdb prot_p1.pdb
> writepsf prot_p1.psf

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