[gmx-users] Topologies for ffamber99 and ions for ffamber99

[Justin A. Lemkul]

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:

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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-- 
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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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