Thank you for reply.
xtc trajectories do work.
Maybe the first time the problem occurred because I was using PyMOL
installed from Linux Mint repository. Now I use SVN one.
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Hi Timofey,
This wiki page is obsolete, current PyMOL includes a recent version of the VMD
plugins, and it can load xtc files (and probably trr too, but I don't have a
test file around). You need to load topology and trajectory in two steps, into
the same object. Example:
load topology.gro, so
The safest way to do that would be to convert your trajectory to a format
readably by PyMOL, with trajectory manipulation tools such as trjconv (in
GROMACS) or catdcd (you can find it in the VMD website). PyMOL recognizes
the AMBER .trj format with the "Load_traj" function, so you can use that:
ht
Is there any way to load .xtc or .trr files into PyMOL to view trajectories?
This user page on the wiki suggest the way, but it looks like it's
outdated and defunct now.
pymolwiki.org/index.php/User:Speleo3/VMD_plugins
Thank you, Bruno and Tsjerk. I found both approaches work very well.
Eric
Frankly, with Pymol, people don't as far as I know. What I usually do
is
determine for the first frame of the individual pdb files (obtained
with
trjconv -sep) the orientation, viewing point and appearance. This I
save
Hi Bruno,
Sure I'm aware of that, but for a bit of a system (as I usually have) and
a good bit of trajectory (as I usually have), that will ask for quite some
memory. Did it a few times, but prefer to use separate pdb's instead.
Though admitted that for small systems, a multistate pdb works great
Hello,
It's possible to convert to a single pdb file containing all the frames
using:
trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr
You can then load it into pymol using:
pymol trajout.pdb
And it will load all the frames.
If you render a movie into png you will have lots of
Hi Yunfeng Hu,
Frankly, with Pymol, people don't as far as I know. What I usually do is
determine for the first frame of the individual pdb files (obtained with
trjconv -sep) the orientation, viewing point and appearance. This I save
in a .pml script. Then with a bit of python code, looping ov
Hi, I wonder if people can give a summary of how pymol makes movies out
of gromacs trr (or xtc) files without having to use all the individual
frame pdb files. Thanks!
Eric
