From: Brian Radak (bradak_at_anl.gov)
Date: Tue Dec 13 2016 - 08:27:28 CST
This all depends on what force field you are using, since the modified
residue names are non-PDB standard as far as I know.
For CHARMM36 the patches are ASPP and GLUP, so I would replace your
mutate commands with the following:
patch GLUP xxxx:20 xxxx:25 xxxx:62
patch ASPP xxxx:65
HTH,
Brian
On 12/13/2016 05:58 AM, Nehad Elsalamouny wrote:
> 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
>
-- 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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