Hi everyone. I am new in the field of molecular dynamic. Would you please help me with altering large DCDs? I want to extract the C-alpha trajectory from my large dcd which is too large to be loaded on VMD or other software. Do you have any code for It? Thank you
It might work using "catdcd" (http://www.ks.uiuc.edu/Development/MDTools/catdcd/). You'd need a textfile which just contains the atom numbers (zero-based) for your C-alphas. This file could be created in VMD using a TCL code such as: (untested)
set a [atomselect top "name CA"]
set atoms [$a get index]
set out [open "indexfile.txt" w]
puts $out $atoms
close $out
In order to be able to work with the resulting file, you might need a PDB file of only the CAs too:
$a writepdb "short.pdb"
Afterwards use catdcd e.g.:
catdcd -o short.dcd -otype dcd -i indexfile.txt -dcd large.dcd
If you know the structure of the binary DCD file, you can read it, and put DCD coordinates into a nested list with a Python script---see the file attached.
You can make a list of atom identifiers of Calpha atoms from your reference PDB file, filter the list of coordinates, and write a multi-PDB file.
It might work using "catdcd" (http://www.ks.uiuc.edu/Development/MDTools/catdcd/). You'd need a textfile which just contains the atom numbers (zero-based) for your C-alphas. This file could be created in VMD using a TCL code such as: (untested)
set a [atomselect top "name CA"]
set atoms [$a get index]
set out [open "indexfile.txt" w]
puts $out $atoms
close $out
In order to be able to work with the resulting file, you might need a PDB file of only the CAs too:
$a writepdb "short.pdb"
Afterwards use catdcd e.g.:
catdcd -o short.dcd -otype dcd -i indexfile.txt -dcd large.dcd
Norman's Answer has the best most efficient approach. Catdcd is a great tool. You should get yourself familiar with.
Dear Norman,
thank you for your detailed answer and introducing catdcd, it solved my problem. I just made some changes in command:
./catdcd -o instead of -ofile
Yes, you are right, I changed the answer correspondingly
Guess I confused the tags with antechamber ^^
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