Re: [AMBER] how to change residue number of several residues in AMBER trajectories

From: Dr. Anselm Horn <>
Date: Thu, 2 Sep 2021 10:23:27 +0200

Dear Ming,

maybe you could setup special trajectories containing just the system of
interest for your individual analysis runs.
For that, you could use cpptraj to strip off the unnecessary residues
from your master trajectory and also write a singe pdb file (e.g. of the
first structure); then use this pdb file to generate a top file via tleap.

Generally, all atoms in a trajectory are numbered in a continous way
internally; a "renumbering" is not possible AFAIK.
Thus, if you have problems to reference the residues of interest, a
preprocessing step might be a simple (yet not the most elegant) solution.



On 09/02/2021 09:25 AM, Ming Tang wrote:
> Dear list,
> I have a tetramer with one ligand bound to each monomer. I want to calculated the binding energy between the two dimers in the tetramer with ligands boundIn my trajectory, all the four ligands are numbered later than the four monomers. But MMGBSA only takes residues with continuous numbers as mark. Is there a way to renumber the trajectory for MMGBSA calculation?
> My case is different with offsetting the residue number discussed in the below post.
> I tried the same way by manually change the residue number, and then use tleap to generate the prmtop file. When I use cpptraj to process my trajectory, it runs but the output trajectory was damaged, the structure was messy.
> Thanks,
> Ming
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Sep 02 2021 - 01:30:03 PDT
Custom Search