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

[Justin A. Lemkul]

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 
following:

http://wiki.gromacs.org/index.php/Parameterization

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

-Justin

> 
> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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