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.hock...@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.hock...@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.hock...@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.hock...@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.hock...@uu.nl
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