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

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 4 12:08:02 CEST 2008

Morteza Khabiri wrote:
> Dear
> 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
> file.
> 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.

You will have to create your own topology if you want to use an all-atom model. 
  See the dozens of posts in the archives about this topic, as well as the 


Note that deriving parameters for new molecules is an advanced topic, and 
requires careful work and lots of time!


> thanks in advance and with kind regards,
> Your sincerely,
> Morteza
> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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