VMD-L Mailing List
From: Brittany Boykin (bzb0031_at_tigermail.auburn.edu)
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.
Department of Chemistry and Biochemistry