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
run
quit
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!
Best,
Matthew
From: laura zhang via AMBER <amber.ambermd.org>
Date: Tuesday, February 7, 2023 at 3:18 PM
To: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
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 $i.prod-unwrap.trj
}
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 '10.prod-unwrap.trj', no error
ERROR) Could not read file 10.prod-unwrap.trj
Unable to load file '10.prod-unwrap.trj' using file type 'trj'.
I am wondering where is wrong in above. How to fix it? Thanks a lot.
Laura
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Received on Tue Feb 07 2023 - 13:00:03 PST
