[gmx-users] pdb2gmx: Amber trajectory conversion
Mark.Abraham at anu.edu.au
Wed Jul 19 04:18:41 CEST 2006
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...
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
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.
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