[gmx-users] Nanotube and DNA interaction

David van der Spoel spoel at xray.bmc.uu.se
Sat Oct 21 09:11:13 CEST 2006

yuzu0501 at sohu.com wrote:
> Hello everyone,
> I am currently studying the interaction between an infinite carbon 
> nanotube and a single stranded DNA molecule. I am using GROMOS96 43a1 
> force fieldfor the DNA molecule. And I am building my system in 
> Viewerpro. However, the pdb2gmx don't seem to work with this pdb file. 
> "ffG43al.n2t" is not found. On the other hand, the x2top is only 
> availble to the CNT part. How can i get the pdb file that can be used 
> with pdb2gmx or how to build the topology for the complex of DNA-CNT?
you are mixing up these things. you have t make separate topologies for 
CNT and DNA. I'm not sure you can use GRMOS for DNA anyway. Then you 
merge the files using a text editor. Read Chapter 5.

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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://folding.bmc.uu.se

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