Re: [AMBER] load amber trj using vmd automatically

From: Matthew Guberman-Pfeffer via AMBER <>
Date: Tue, 7 Feb 2023 20:45:12 +0000

Laura, a quick dirty fix is the following

Use CPPTRAJ to concatenate the trajectories and convert to dcd

parm <topology>.parm7
trajin <traj1>.nc
trajin <traj2>.nc

Trajout outtraj.dcd CHARMM


Then, load the dcd into VMD; you can use the parm7 file (no need to convert to psf)

vmd -parm7 < <topology>.parm7 -dcd <outtraj>.dcd waitfor all

Hope that helps!


From: laura zhang via AMBER <>
Date: Tuesday, February 7, 2023 at 3:18 PM
To: Matthew Guberman-Pfeffer via AMBER <>
Subject: [AMBER] load amber trj using vmd automatically
*Message sent from a system outside of UConn.*

Dear Amber users,

I generated multiple amber trj files. I tried to load all the trj files using a tcl code with the content as below:

set mol [mol new pcsk9.wet.complex.parm7 type parm7]
mol addfile pcsk9.wet.complex.pdb
for {set i 10 } {$i < 13 } { incr i } {
mol addfile $

Then I typed the following on the command line to run it:
> vmd -dispdev text -e add_dcd.tcl

But I got the following error message on the screen:

gromacsplugin) Cannot read header fromm '', no error
ERROR) Could not read file
Unable to load file '' using file type 'trj'.

I am wondering where is wrong in above. How to fix it? Thanks a lot.

AMBER mailing list
AMBER mailing list
Received on Tue Feb 07 2023 - 13:00:03 PST
Custom Search