[gmx-users] pyroglutamate in gromos53a6

[Tsjerk Wassenaar]

Hi Henry,

Apparently NPCA is not listed as being protein, so pdb2gmx assumes
that the chain begins with GLY. Add NPCA to the file residuetypes.dat
one directory up, with the designation 'Protein'. I think that should
solve it.

Groetjes,

Tsjerk

On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking <H.G.Hocking at uu.nl> wrote:
> Thank you Tsjerk,
> I am now trying with amber99.ff but have encountered the following problem:
> My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp
> and have updated aminoacids.r2b to include NPCA and I've even added an entry
> in aminoacids.hdb for NPCA. Yet when I generate my itp/gro files using
> pdb2gmx, the NPCA is recognises (all atoms are there) but the second residue
> [ GLY ] is now changed to [ NGLY ] in the itp file despite still being the
> second residue in the gro file. As a test, if I remove NGLY from
> aminoacids.r2b it complains that 'there is no residue type for 'GLY' as a
> starting terminus' thus ignoring that the first residue of my chain is in
> fact NPCA.
> What could be going on here? The -ter flag has no effect here as I noticed
> that for all amber99XX.ff the aminoacids.n.tdb files are empty.
> Cheers,
> Henry
>
>
>
> On 22 Nov 2011, at 18:17, Tsjerk Wassenaar wrote:
>
> Hi Henry,
>
> That would be a bit of a wild west approach. A better approximation
> would be taking the charges from the backbone amide group, as it is
> just an amide with on either side aliphatic carbons. Doing it properly
> is a bit more involved, as for the G53a6 FF you need to choose
> parameters giving the right free enthalpy of solvation.
>
> Groetjes,
>
> Tsjerk
>
> On Tue, Nov 22, 2011 at 5:10 PM, Henry Hocking <H.G.Hocking at uu.nl> wrote:
>
> Dear all,
>
> Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA)
>
> ?
>
> Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a
>
> way I could adapt these to gromos53a6.ff?
>
> Can I use, for example, the gromos53a6.ff atom types from glutamine,
>
> add/remove appropriate bonds / angles / impropers and then take the
>
> corresponding charge values from my amber99.ff/aminoacid.rtp file. I assume
>
> that what I've just suggested is the cowboy method and that in reality it is
>
> not that straightforward, right?
>
> Kind regards,
>
> Henry
>
> --------------------------------------------------------
>
> Henry Hocking, PhD
>
> Utrecht University
>
> Bijvoet Center for Biomolecular Research
>
> Padualaan 8
>
> 3584 CH Utrecht, The Netherlands
>
> Phone: +31-30-2532875
>
> Fax: +31-30-253 7623
>
> E-mail: H.G.Hocking at uu.nl
>
>
>
>
>
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> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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> --------------------------------------------------------
> Henry Hocking, PhD
> Utrecht University
> Bijvoet Center for Biomolecular Research
> Padualaan 8
> 3584 CH Utrecht, The Netherlands
> Phone: +31-30-2532875
> Fax: +31-30-253 7623
> E-mail: H.G.Hocking at uu.nl
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands