[gmx-users] pyroglutamate in gromos53a6

[Henry Hocking]

Thank you Tsjerk,

Now it works !

Cheers,

Henry

On 24 Nov 2011, at 23:11, Tsjerk Wassenaar wrote:

> 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
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
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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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