Dear All,
I apologise for posting this to the lammps mail-list; I have tried subscribing to the vmd list, however, even though I received the information that my subscription is activated, I do not seem to get any emails from VMD users. Therefore, I hope that some of You might use VMD for lammps visualisation.
My problem is creating a contact map for atoms of two non-amino acid polymer chains; when I try the GUI "data analysis --> contact map" this does not seem to recognise any atoms in my simulation because these are not amino acids.
Does anybody by any chance know how I could possibly overcome this problem?
Thank you very much in advance!
Anna
Dear All,
I apologise for posting this to the lammps mail-list; I have tried
subscribing to the vmd list, however, even though I received the
information that my subscription is activated, I do not seem to get any
emails from VMD users. Therefore, I hope that some of You might use VMD
for lammps visualisation.
My problem is creating a contact map for atoms of two non-amino acid
polymer chains; when I try the GUI "data analysis --> contact map" this
does not seem to recognise any atoms in my simulation because these are
not amino acids.
Does anybody by any chance know how I could possibly overcome this problem?
yes. as you already noticed, the contactmap plugin, like most "older" VMD stuff,
assumes deep inside that you are working on peptides, thus you have to make
your polymers look like peptides to VMD.
the contactmap plugin operates only on atoms that are named CA and
assumes that there is only one of them per "residue", so you have to
simulate this. assuming that you want the contact map between _all_
atoms in your polymer, then you'd have to execute the following VMD
script code in the vmd console:
set sel [atomselect top all]
$sel set name CA
$sel set resid [$sel get serial]
mol reanalyze top
$sel delete
unset sel
then try using contactmap again and let me know if that works.
if you want to do this more often, you can put this piece of code
in a file, say fake_peptide.tcl and then pull this in via: play fake_peptide.tcl
cheers,
axel.