Re: protonating ASP and GLU

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 13 2016 - 13:06:05 CST

Hello Nehad, I believe you're better off using Leap, or in general the
AMBER tool suite to prepare an AMBER topology. PsfGen is best suited for
CHARMM-format force field files.

Giacomo

On Tue, Dec 13, 2016 at 1:48 PM, Nehad Elsalamouny <nehade_at_uow.edu.au>
wrote:

> I am using amber force field so what will be the modified residue names in
> that case?
>
> Nehad
>
> On Dec 14, 2016, at 1:27 AM, Brian Radak <bradak_at_anl.gov> wrote:
>
> 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
>
>

-- 
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
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*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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