[gmx-users] Terminal groups problem

Oleg V. Stroganov Oleg_Stroganov at newmail.ru
Wed Oct 8 13:49:00 CEST 2003

Hello , gmx-users

My task is not only to get suitable parameterization of the molecule.
I want to increase the simulation timestep up to 7 femtoseconds. For
this purpose it is necessary to use a dummy constructions for terminal
NH2 group. But when I tried to include dummy atoms, MN1 MN2 into
itp-file (the same way as described recently in Senthil Kandasamy
letter), pdb2gmx produced an error:
Fatal error: Automatic parameter generation not supported for Dummy3

On the other hand, I have previously used automatically generated dummy
atoms for derivatives of some aminoacids. All parameters were added into
ffG43a1.rtp and aminoacids.dat.

So, I want Gromacs to 1) recognize all terminal groups and 2) automatically add
dummy constructions for terminal NH2 group.


Best regards,
 Oleg                          mailto:Oleg_Stroganov at newmail.ru

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