Date: Thu, 31 Aug 2000 12:03:07 -0600
From: "Thomas E. Cheatham, III"
Subject: Re: rdparm/ptraj


> I have a truncated octahedron as a box and I would like to process my
> trajectories with rdparm/ptraj to translate all the waters back to
> the original box. I have found out that the command "transform" or
> "processt" isn't working under version no:6 of AMBER. Is it any easy
> way to do this.

I haven't updated the DNA polyA-polyT tutorial to use the newer means to
image trajectories. Therefore users of this specific tutorial (in
particular the last section on analysis) are probably being slightly
misled on the tools-- however the general ideas and issues to worry
about are relevant none-the-less. I hope remedy this deficiency of the
tutorial soon with respect to ptraj.

The "transform" or "processt" commands of rdparm are outdated, inflexible,
not very general; also, these were never coded up for shapes other than
orthorhombic (i.e. 90.0 box angles). Newer versions of the
imaging are significantly more general and can handle any triclinic shape,
however this is all though the "ptraj" functionality...

Since these questions come up fairly frequently, I thought I would send
this information out to you and the entire list to (a) briefly describe
the more recent versions of rdparm/ptraj, point to documentation and where
people even without AMBER 6.0 can get the latest version and (b) show a
few examples for imaging triclinic, etc. that I commonly use.

(a) rdparm/ptraj is a single program that evolved out of a tool I
developed as a graduate student in Kollman's group to analyze AMBER prmtop
files. The rdparm part is really just for looking at AMBER prmtop files
and doing a few other specialized things such as:

-- removing waters from a prmtop file with the "testwater" command
-- printing out information about various bonds, atoms, dihedrals, etc,
-- checking out coordinates to make sure they are not corrupted

The code was kind of clunky, so I built a new part of it called
"ptraj" that was set up to analyze trajectories. Since it was based on
the same prmtop functionality as rdparm, it is all part of the same
program/code. Which functionality is run at runtime depends on the name
of the executable. This is discussed more in the ptraj.html and
rdparm.html files that are attached.

ptraj is set up to read a variety of (optionally compressed) trajectory
files (including PDB, AMBER restart and trajectory, CHARMM trajectory
and the Scripps binary format coordinate files) and perform "actions" on
each coordinate set read in. Specific actions are centering, imaging, RMS
fitting, measuring angles, etc. See the attached ptraj.html file for more
information. Since the code is fairly straightforward and commented to a
degree, others have also joined into the development effort.

Current versions of the software (and various force field files
converted to CHARMM format) are available in the near term under the link

http://hnu.pharm.utah.edu/medchem/cheatham/software.html

If people have questions about ptraj/rdparm, particularly referring to
problems or inadequacies of the code, please post them to the AMBER mail
reflector or to me personally at "cheatham@chpc.utah.edu" and I will try
to respond...

(b) Some common examples. Trajectory files with explicit solvent are
typically very large and broken up into a series of files. In addition,
imaging may or may not have been performed on the trajectory by sander
(and even if it was, molecules may have been imaged separately, such as
DNA, leading to cases where the molecules appear in different boxes and
look like they have suddenly blown up or denatured). So, a common script
reads in all the trajectory files, creates a single output file stripped
of the waters, performs centering, imaging and RMS fitting. Here is such
a script:

trajin mdcrd.1.Z
trajin mdcrd.2.Z
trajin mdcrd.3.Z
trajin mdcrd.4.Z
trajin mdcrd.5.Z
trajin mdcrd.6.Z 1 100 1
trajout strip.traj nobox
center :1-10 mass origin
image origin center
center :1-20 mass origin
image origin center
rms first mass out rms_to_first.data :1-20
average avg.pdb :1-20 pdb
strip :WAT

This will:

(1) read in all frames of trajectory files mdcrd.1.Z -> mdcrd.5.Z and
only the first 100 frames of mdcrd.6.Z
(2) create a new AMBER trajectory file called strip.traj that doesn't
contain the periodic box information (so I can use a prmtop file
created without box information for subsequent processing of this file).
(3) center residues 1-10 to the origin using the center of mass
(4) image atoms using the center of mass of each molecule with the box
center at the origin

[we do these two steps above to solve the split molecule problem
under the assumption that residues 1-10 represent the first molecule
and residues 11-20 represent the second molecule and logically we
want them to be close to each other as in a DNA 10-mer duplex. To
clarify this a little, sander images by molecule. When building a
solute such as a DNA duplex or protein-ligand, the separate strands
or protein and ligand are each in a separate molecule. Imaging to
bring a molecule back in the box may make it appear that one of the
strands or ligands has suddenly jumped away from the other or protein
(which it has); this is no problem in a periodic system, however when
looking at movies or calculating RMSd values which do not necessarily
image to keep the logically associated molecules together will lead
to apparent anomolies as is constantly discussed on the reflector...]

(5) center residues 1-20 (the whole solute)
(6) image again
(7) RMS fit each coordinate set to the first set
(8) create an average structure for residues 1-20 over the whole time in
PDB format
(9) strip all residues named "WAT" from the output trajectory


Now for triclinic, in the case of AMBER generated trajectories, the box
shape should be picked up automatically and imaging done as
appropriate. However, this imaging is to a triclinic unit cell rather
than the more familiar (near spherical) truncated octahedron or rhombic
dodecahedron shapes. To get the more familiar shape, or to image atoms
not by shape but by proximity to the center of mass of the box or of a
particular atom selection, the keyword "familiar" can be added to the
image command.

I hope this helps.

Thomas E. Cheatham, III