Hi Arturas!
A - relatively - easy way to read DCDs into PyMOL is:
* Convert the .dcd to .trr using catdcd 4.0
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/). At the same time you can
concatenate multiple .dcd files, remove solvent, skip frames, etc.
* Convert the .trr file to a multi-model .pdb file using trjconv from the
Gromacs package (http://www.gromacs.org/) Here you can select eg. desired
residues (using make_ndx), skip frames, and align each frame to a reference
structure before writing the pdb file.
Using two programs may seem a bit complicated, but most likely you want to
concatenate files, remove solvent or do other processing anyway, so I think it
is ok :-)
This works quite nicely for me. If you want to look at every single frame of a
long MD with many atoms, you may run into problems with very large pdb files,
though.
Having the trajectory as a .trr file also gives the possibility of using
Gromacs' analysis tools, such as g_rms or g_rmsf.
There are some examples below...
Cheers,
Esben
-
# the structure is in system.pdb, system.psf and trajectories in
-0100.dcd ... 0900-1000.dcd.
# creating the stripped pdb file (removing solvent (residues called TIP3)):
grep -v TIP ../system.pdb solute.pdb
# creating the index file for catdcd (for removing solvent):
awk '/ATOM/ {print $2-1}' solute.pdb solute.idx
# making the stripped file in gromacs format.
/z/linux/catdcd4/LINUX/bin/catdcd4.0/catdcd -o wt_strip.trr -otype trr -i
solut.idx ../-0100.dcd ../0100-0200.dcd ../0200-0300.dcd ../0300-0400.dcd
../0400-0500.dcd ../0500-0600.dcd ../0600-0700.dcd ../0700-0800.dcd
../0800-0900.dcd ./0900-1000.dcd
--
# The per-residue rms and pdb file for putty cartoon
g_rmsf -f wt_strip.trr -s solute.pdb -oq test.pdb
# select group 4 for backbone
# load test.pdb in PyMOL and show it as putty cartoon:
pymol load test.pdb
pymol cartoon putty, test
pymol show cartoon, test
pymol hide lines, test
# The overall rmsd as a function of time
g_rms -f wt_strip.trr -s solute.pdb
# selecet group 0, compare to 1, and select group 0 again
# The resulting rmsd.xvg can be shown directly with xmgrace
(http://plasma-gate.weizmann.ac.il/Grace/):
xmgrace rmsd.xvg
-
#Showing MD ensemble of specific residues (here 100,101,102,103,200,201):
# run make_ndx
make_ndx -f solute.pdb -o site.ndx
# make a new group
r 100 101 102 103 200 201
# delete the other groups:
keep 14
# call it site
name 0 site
# save and quit:
q
# run trjconv to get a pdb file with every 100th frame for the site residues:
trjconv -f wt_strip.trr -o site.pdb -s solute.pdb -n site.ndx -fit
rot+trans-skip 100
# load site.pdb and solute.pdb in pymol
pymol load site.pdb
pymol load solute.pdb
# use a similar selection in pymol to align it to the reference structure:
pymol select solute and resi 100+101+102+103+200+201
pymol align siteCA, seleCA
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Warren DeLano
Sent: Fri 2006-02-10 20:08
To: ziemy...@osu.edu; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] NAMD/dcd
Arturas,
DCD suppot? Not yet -- we need someone to either donate, develop, or
fund code to support this key MD trajectory format.
Cheers,
warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
zie...@ecr6.ohio-state.edu
Sent: Friday, February 10, 2006 10:59 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] NAMD/dcd
HI !
I new one with PyMol and found it very promising for my
works. However, I need analyze MD trajectories DCD from NAMD.
Is there any clue to load DCD's, as manual talks only abaout
Amber format ?
Best
Arturas Z.
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