[gmx-users] deprotonation and DNA

Erik Marklund erikm at xray.bmc.uu.se
Tue Nov 23 10:36:26 CET 2010

luo jinghui skrev 2010-11-23 10.31:
> Hi,
>    I am running DNA simulation  with amber force field. I did 
> deprotonation on some of adenine group and then add some ions to get 
> system without charge. Do you think this system will be  suitable for 
> MD simulation?
> regards,
> Jinghui

Yes, maybe. It depends how the deprotonation was done. More 
specifically: where you got the parameters for the deprotonated adenines.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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