[gmx-users] Topologies for ffamber99 and ions for ffamber99
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 7 16:01:32 CEST 2009
tanos at ime.eb.br 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:
> 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
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.
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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