Re: selectively assign HIE or HID for HIS residues

From: Vermaas, Joshua (
Date: Tue Dec 06 2016 - 11:03:38 CST

Also, if these names are in the input PDB, you can avoid the aliasing step altogether. So if for instance you were to use VMD to rename those residues:

set hsdsel [atomselect top "resname HIS and resid 57 91 99 100 165 241"]
$hsdsel set resname HSD
set hsesel [atomselect top "resname HIS and resid 37 170 233"]
$hsesel set resname HSE
set allsel [atomselect top "all"]
$allsel writepdb xxx.pdb

you could then remove those pdbalias lines.


On 12/05/2016 09:24 PM, Brian Radak wrote:

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



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
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

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.



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

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