Re: protonation of some histidine residues

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Sep 14 2007 - 16:53:10 CDT

Hi,

You're getting this error because HSP is not a patch. You can either
"mutate" the residue to HSP or change the name (in your original pdb
files) of HIS to HSP (*only* to the Histidines you want to be
protonated).

Cheers, Michel

2007/9/14, mdametto_at_mail.usf.edu <mdametto_at_mail.usf.edu>:
> 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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