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 0000-0100.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 ../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: 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. > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files for problems? Stop! Download the new AJAX > search engine that makes searching your log files as easy as > surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=k&kid3432&bid#0486&dat1642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
