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
--
---------------------------------------------------
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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