Dallas B. Warren wrote:
The script that deals with converting trajectories is trjconv. Have a
look at the documentation, that will show you the formats it can handle,
no idea what Amber format is, but as long as you can get it into one of
the ones it can use should be fine.
trjconv can't handle the usual Amber DCD format
Plus, with g_cluster I suspect you
will require a topology file to be able to do the analysis, which will
be your major sticking point.
Actually it needs a structure file - in man g_cluster the FILES section
indicates that the -s option needs one of many formats that imply
structure and masses, and a full .tpr is thus not required.
Note that pdb2gmx converts pdb coordinate files to generate a topology
file (and the residues/molecules have to be known by the database
otherwise you have to make by hand etc).
Here's the text of an email I sent to a group member who was grappling
with this general AMBER conversion issue just last week...
Mark
------------------------
Hi Sue,
Issue 1 - using gromacs cluster tools with amber trajectories.
Converting the trajectory is easy - load the structure into VMD, import
the amber trajectory and choose Save Coordinates from the File menu and
choose the "trr" file format. There's an ugly Plan B if that doesn't
work, but I won't describe it now.
You'll also need any structure file that will supply atom names and
stuff, and use the gromacs tool make_ndx to make a index file that
basically describes the subset of atoms you actually want to do the
analysis on - i.e. the atoms for the RMSD.
Those three files will be enough to run g_cluster with, so actually it
should be very painless for you. The most annoying bit would be
transferring the trajectory files to and from ac to use vmd on them -
hang on, they have vmd 1.8.2 available on ac ("module load vmd") if you
have X-Windows available (e.g. markov or valera console) then you can
even do that conversion remotely.
I'd suggest getting the gromacs manual from their website
http://www.gromacs.org/. The man pages for their tools are included
there, but "man make_ndx" and "man g_cluster" will give you most of what
you need to know and you're welcome to ask me for clarification. Note
that on those manpages the SYNOPSIS section implies particular filename
extensions - actually there's normally a range of possible formats that
are described fully in the FILES section for each option. In particular,
I don't believe you'll need to generate a .tpr file - a .pdb produced by
ambpdb ought to suffice.
Issue 2 - clustering and VMD
If you look here http://www.ks.uiuc.edu/Research/vmd/plugins/ there is a
clustering-result visualisation package available for VMD but it
requires the use of two clustering codes I know nothing about, at least
one of which will cost money - XCluster.
I think the gromacs solution is the way to go initially. I am not sure
how to generate views of simultaneous superpositions in VMD, but the
gromacs tool trjconv makes it easy to extract a series of snapshots from
the trajectory that correspond to a cluster into (say) the same PDB file
and now it should only be a matter of massaging that to get VMD to show
them superposed.
Oh, and there is also KClust http://mmtsb.scripps.edu/doc/kclust.html
which might be easiest of all, but you're on your own here.
Mark
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