[gmx-users] virtual site generation for backbone hydrogen

Jochen Hub jhub at gwdg.de
Mon Dec 17 17:28:27 CET 2012

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 

I have already added RETK into residuetypes.dat, and there are entries 
in the rtp and hdb.

Many thanks in advance for any help,

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

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