From: Brittany Boykin (
Date: Sat Nov 29 2014 - 14:38:49 CST


I am new to VMD and I am trying to use it to build a molecule (organic linker and two single-stranded DNA). They need to be attached by a phosphate group at the 5' end on each side of the linker. Is it possible to form a bond between the two oxygen ends of the linker and the 5'end of the phosphate group and if so how do you go about this? I would like to run this created structure through AMBER tleap and then Molecular Dynamics.

Also, I tried numerous times to create a psf for my linker and DNA and it does not seem to work as easily as if it were a protein.

Can someone please help, this is for a class project and unfortunately I have ran out of options as well as time.


Brittany Boykin
Graduate Student
Auburn University
Department of Chemistry and Biochemistry
c: (404)545.1036