[AMBER] nc files contain lesser number of atoms compared to prmtop

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Thu, 17 Dec 2020 11:46:53 +0530

Dear all,

I have done a 100 ns NVT simulation on a protein-DNA system and used the
restart file to do 30ns gaussian accelerated MD on to the system using the
script attached. After completion, upon running cpptraj to obtain the rmsd
of the system using the GaMD trajectory, I got the error that there are
only 22 atoms in the nc file while, 2,00,000 atoms in the prmtop. I had
used the same prmtop for running the GaMD as well. Could someone suggest
why this might be happening? I had tried to visualize but was not possible
due to exactly the same issue.

Sruthi Sudhakar

AMBER mailing list

Received on Wed Dec 16 2020 - 22:30:02 PST
Custom Search