[email protected] wrote:
Dear gmx users,
I am trying to perform MD simulations of a DNA dodecamer complexed
with some ligands but I facing some problems to generate the ligands
topologies and insert Na ions to neutralize the system ! I have built
the first ligand.itp file by hand, what is very time consuming. So I
wonder if someone know a software or server (like PRODRG) able to
generate ligand topologies to the ffamber99 force field.
There are some tools in the User Contributions section of the website:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions
Also, I am wondering how to include the ions topology in the GROMACS
file ions.itp in order to make ffamber99 force field recognize the ion
topology.
Follow the format of ions.itp; you will need to include a section starting with
#ifdef _FF_AMBER and fill out the entries for the ions you're using, according
to the naming in the Amber force fields. The manual is your friend here.
-Justin
With the best regards,
Tanos C. C. Franca.
Laboratory of Molecular Modeling Applyed to the Chemical and
Biological Defense (LMMCB)
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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