[gmx-users] How generate top file with all hydrogen atomes

Morteza Khabiri khabiri at greentech.cz
Thu Sep 4 11:34:22 CEST 2008


I have been trying to use the PRODRG server to generate GROMACS topology
files for some organic molecules.But unfortunately the PRODRG server
automatically deletes all hydrogens and only (re)creates "polar"
hydrogens. However, I also want to "keep" the H atoms conected to the
aromatic carbons but it doesn't have any separated H atom at generated top
wHITH THIS TOP file i couldn't use other forcefields becuase just the
groamacs is the unified atom and others attent to H atoms separately.
Is there any way to solve this problem.

thanks in advance and with kind regards,

Your sincerely,


Ph.D student of Biophysics
Laboratory of High performance computing
Institute of Systems Biology and Ecology ASCR
Institute of Physical Biology,
University of South Bohemia
Zamek 136 373 33, Nove Hrady
Czech Republic
Email: Khabiri at greentech.cz
mobile: +420 773 903 109

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