From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 06 2016 - 16:08:47 CST
You could use the "mutate" command for this:
segment xxxx {
pdb xxxx.pdb
mutate 37 HIE
mutate 57 HID
...
}
You may still need "residue HIS HID" to keep the "pdb" command from
complaining about HIS being unknown.
Jim
On Tue, 6 Dec 2016, 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
>
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