[gmx-users] .pdb file for DNA

Dear All, I want to simulate interaction between single strand dna and cnt. I tried to use Biomer (from case group webpage), but it's not working. When I try to open B.html in my browser, I get a blank page. Could anyone please tell me if there is another way to generate .pbd file for dna? Th

Re: [gmx-users] zero SOL molecules

sarah k wrote: Dear all, I am adding Nitrogen box instead of water molecules to my protein. Based on your guidelines I generated the coordination and topology file of nitrogen. Then I used the following command: genbox -cp A_newbox -ci -42000mol N2C.gro -o A_solv.gro -p topol.top N2C.gro

[gmx-users] zero SOL molecules

Dear all, I am adding Nitrogen box instead of water molecules to my protein. Based on your guidelines I generated the coordination and topology file of nitrogen. Then I used the following command: genbox -cp A_newbox -ci -42000mol N2C.gro -o A_solv.gro -p topol.top N2C.gro is my new file made man