[gmx-users] virtual site generation for backbone hydrogen

[Jochen Hub]

Sorry, I found the error. There was a bond -C  N missing in the rtp file.

Cheers,
Jochen

Am 12/17/12 5:28 PM, schrieb Jochen Hub:
> Hi all,
>
> I try to generate a topology using pdb2gmx of a protein that contains a
> non-native amino acid, that is "lysine with some more atoms", which is
> treated a one amino acid RETK.
>
> Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a
> constraint is generated between the backbone CA and H (that gives an
> error later grompp since the constraint type CT-H is not defined).
>
> [ atoms ]
> ...
>    3603          H    216   RETK      H   3241     0.2747      1.008
>    3604         CT    216   RETK     CA   3242      -0.24     13.018
> [ constraints ]
>   3603  3604     2
>
> If the non-native aa is replaced by a LYS, pdb2gmx generates instead:
>
> [ virtual_sites3 ]
>   3603  3602  3600  3604     2
>
> I now wonder how to tell pdb2gmx that RETK should be treated as any
> other amino acid, that is that the backbone-H should be turned into a
> virtual_site3.
>
> I have already added RETK into residuetypes.dat, and there are entries
> in the rtp and hdb.
>
> Many thanks in advance for any help,
> Jochen
>
>
>

-- 
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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