[gmx-users] How to get an infinite DNA topology

[elixer at mail.ustc.edu.cn]

Hello everyone,
I am working on a MD simulation using AMBER99 force field with gromacs in a system including a very long A-type DNA fragment. My plan is to build a cell containing exact 11 DNA base bair (which is a circle of A-type DNA), and with periodic boundary conditions to get an infinite DNA topology. But the problem is that pdb2gmx reports a fatal error: Atom P in residue DA 2 (which is my first DNA residue from 5' end) was not found in rtp entry DA5 with 30 atoms while sorting atoms. It looks like the program is trying to find the residue of 5' end in a DNA fragment with limitid length, which is not existed in my system. The 5' end DNA residue is a little different from a normal DNA residue, like it is short of a P atom, which is probably why the error occurs. So is there a way to prevent the program from trying to find the 5' end DNA fragment? Or is there any other way to build an infinite DNA topology?
Best regards,
Elixer