[gmx-users] virtual site generation for backbone hydrogen

[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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