From: Nehad Elsalamouny (nehade_at_uow.edu.au)
Date: Tue Dec 13 2016 - 05:58:51 CST
Dear NAMD users,
I need to generate a psf file with protonated ASP and GLU residues using the following script:
package require psfgen
topology ../../xxxx.rtf
topology ../../xxxx.rtf
topology ../../xxxx.rtf
pdbalias atom ILE CD1 CD
pdbalias residue HIS HID
segment xxxx {
pdb xxxx.pdb
mutate 20 GLH
mutate 25 GLH
mutate 62A GLH
mutate 65 ASH
}
coordpdb xxxx.pdb xxxx
regenerate resids
guesscoord
patch DISU uPA:62 uPA:46
patch DISU uPA:125 uPA:54
patch DISU uPA:219 uPA:150
patch DISU uPA:198 uPA:182
patch DISU uPA:238 uPA:209
segment xxxx {first none; last none; auto none; pub xxxx.pdb}
coordpdb xxxx.pdb xxxx
segment xxxx {first none; last none; auto none; pdb xxxx.pdb}
coordpdb xxxx.pdb xxxx
segment xxxxx {first NONE; last NONE; auto none; pdb xxxxx.pdb}
coordpdb xxxxx.pdb xxxx
guesscoord
writepdb xxxxx.pdb
writepsf xxxxx.psf
The mutate command works well for for GLU and they are converted to GLH, however I receive an error message for ASP: unknown residue type ASH.
What is the problem? And how can I protonate the ASP?
Thanks,
Nehad
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