Re: selectively assign HIE or HID for HIS residues

From: Brian Radak (bradak_at_anl.gov)
Date: Mon Dec 05 2016 - 22:13:09 CST

The CHARMM residue names are HSD, HSE, and HSP.

Cheers,

Brian

On 12/05/2016 08:19 PM, Nehad Elsalamouny wrote:
> Dear NAMD users,
>
> I am trying to generate a psf file using the following script:
>
> package require psfgen
> topology ../../xxxxxxx.rtf
> topology ../../xxxxxxx.rtf
> topology ../../xxxxxxx.rtf
>
> pdbalias atom ILE CD1 CD
> pdbalias residue HIS HID
>
> segment xxxx {pdb xxxx.pdb}
> coordpdb xxxx.pdb xxxx
> regenerate resids
> guesscoord
> patch DISU xxxx:62 xxxx:46
> patch DISU xxxx:125 xxxx:54
> patch DISU xxxx:219 xxxx:150
> patch DISU xxxx:198 xxxx:182
> patch DISU xxxx:238 xxxx:209
>
> segment xxxx {first none; last none; auto none; pdb xxxx.pdb}
> coordpdb xxxx.pdb xxxx
> segment SO4 {first none; last none; auto none; pdb SO4.pdb}
> coordpdb SO4.pdb SO4
> segment XWAT {first NONE; last NONE; auto none; pdb XWAT_rename.pdb}
> coordpdb XWAT_rename.pdb XWAT
> guesscoord
>
> writepdb xxxx.pdb
> writepsf xxxx.psf
>
> Actually everything goes well and the psf and pdb files are generated.
> I want to ask if I need to selectively assign HIE or HID for HIS
> residues i.e.: substitute (pdbalias residue HIS HID) with:
>
> pdbalias residue HIS 37 HIE
>
> pdbalias residue HIS 57 HID
>
> pdbalias residue HIS 91 HID
>
> pdbalias residue HIS 99 HID
>
> pdbalias residue HIS 100 HID
>
> pdbalias residue HIS 165 HID
>
> pdbalias residue HIS 170B HIE
>
> pdbalias residue HIS 233 HIE
>
> pdbalias residue HIS 241 HID
>
>
> How can I write this in my script? I have tried a lot and I fail. I
> get an error msg: unknown residue type HIS.
>
> Thanks,
>
> Nehad

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

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