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: [EMAIL PROTECTED]
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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