VMD-L Mailing List

From: Ananya Nayak (ananyanayak_at_tifrh.res.in)
Date: Tue Dec 12 2023 - 23:06:48 CST

Hi, I'm using the VMD pathways plugin for the first time. I'm analyzing a
trajectory, these are few issues I'm facing while doing it. I'll be
grateful for any insight.
1. When I'm giving the trajectory with PSF file with water in it, it shows
the error " missing operator at _@_ in expression "7093 _@_17093+1". And
I've three systems it's same for all of them; only the expression line
number changes. But if I remove the hydrogen from water, there is no
problem; it runs fine. Also, without water it runs fine. I've tried to give
'with h' and 'without h' in the command line; while without h it gives me
the above missing operator error; with h it shows the "warning: pathcore
shows errors, segmentation violation and child process killed for every
frame. Zero pathways found".
But I've tried the systems in all the above mentioned conditions even in
vacuum too and I got some pathways. I'm unable to figure out what is the
problem when I'm adding the Hydrogen of waters.
2. I'm running the VMD in text mode in a cluster which doesn't have a
graphical interface, so after all the frames are analyzed it can't generate
a movie and exits, the next step should be the fluctuation analysis, but it
doesn't go there. Is there a way to do that?