Re: [gmx-users] DNA simulation

2012-12-11 Thread Justin Lemkul 



On 12/11/12 5:22 AM, delara aghaie wrote:

Dear Gromacs users

I want to simulate dobule strand DNA using gromacs. I have read that I should 
use amber forcefield for DNA simulation and I have crossed a web page 
explaining some parameters which I should change in gromacs package to become 
compatible with this amber force filed.



What changes are suggested?  Note that the previous ffamber ports are no longer 
necessary, as native support for AMBER force fields has been present since 
version 4.5.




1) I want to know that is it possible to use straightly pdb2gmx command on pdf 
file of DNA (taken fron protein data bank) and choose amber forcefiled for that?



Yes.


2) Are that changes necessary?



Probably not, but since you haven't said what those changes are, no one can give 
a definitive answer here.




3) If pdb2gmx does not give error how can I make sure about the correctness of 
procedure.


pdb2gmx will read in the parameters from whatever force field you choose.  If it 
succeeds with no errors, then all of those parameters have been applied 
successfully.  Is there some reason you believe there is a problem?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] DNA SIMULATION

2009-07-18 Thread David van der Spoel 

Morteza Khabiri wrote:

Dear gmxuser

Does somebody knows how to simulate the DNA in gromacs??
I know it is so general question but I need some hint.


Check out the amber force field with gromacs web site.

Thanks


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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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