[gmx-users] DNA Simulation

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 18 10:07:13 CET 2006

ramadugu at sscu.iisc.ernet.in wrote:
> Dear Gromacs users,
>    I'm trying to run a simulation with DNA and drug. I have generated 
> the top file for the drug using the online server. But when I'm trying 
> to generate the gms and top files for the DNA I'm unable to do using the 
> pdb2gmx with any of the force fields. Could anyone please tell if I can 
> get any tutorial for the DNA-drug simulation.
try the amber force field from the STanford group.

> Thanks for ur help in advance.
> Regards,
>  Sai
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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