From: Nehad Elsalamouny (nehade_at_uow.edu.au)
Date: Mon Dec 05 2016 - 20:19:44 CST
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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