[gmx-users] pyroglutamate in gromos53a6

[Henry Hocking]

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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