RE: [PyMOL] NAMD/dcd

[EPF \(E. P. Friis\) <EP...@no...>]

Hi Arturas!


A - relatively - easy way to read DCDs into PyMOL is:=20

* 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 :-) =20

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.=20

Having the trajectory as a .trr file also gives the possibility of using =
Gromacs' analysis tools, such as g_rms or g_rmsf.=20


There are some examples below...


Cheers,

Esben


-----------------

# the structure is in "system.pdb", "system.psf" and trajectories in =
0000-0100.dcd ... 0900-1000.dcd.=20

# 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 ../0000-0100.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 site////CA, sele////CA




-----Original Message-----
From: pym...@li... on behalf of Warren DeLano
Sent: Fri 2006-02-10 20:08
To: zie...@os...; pym...@li...
Subject: RE: [PyMOL] NAMD/dcd
=20
Arturas,

DCD suppot?  Not yet -- we need someone to either donate, develop, or
fund code to support this key MD trajectory format.=20

Cheers,
warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> zi...@ec...
> Sent: Friday, February 10, 2006 10:59 AM
> To: pym...@li...
> Subject: [PyMOL] NAMD/dcd
>=20
> HI !
>=20
> I new one with PyMol and found it very promising for my=20
> works. However, I need analyze MD trajectories DCD from NAMD.=20
>=20
> Is there any clue to load DCD's, as manual talks only abaout=20
> Amber format ?
>=20
> Best
> Arturas Z.
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