From: Nehad Elsalamouny (nehade_at_uow.edu.au)
Date: Tue Dec 06 2016 - 15:03:47 CST
Thanks Josh and Brian,
I thought I can write this as pdbalias but it seems that the easiest way is to rename them in the pdb file.
Kind regards,
Nehad
> On Dec 7, 2016, at 4:03 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
>
> 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.
>
> -Josh
>
> On 12/05/2016 09:24 PM, Brian Radak wrote:
>
> The CHARMM residue names are HSD, HSE, and HSP.
>
> Cheers,
>
> Brian
>
> 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
> 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
>
> --
> 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<mailto:brian.radak_at_anl.gov>
>
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