#7 SCD of unnatural lipid tail

[Shashank Pant]

Hello,

I am trying to calculate the lipid order parameter of an unnatural lipid. Essentially, I have a myristoyl tail attached to a residue and I want to calculated SCD of this tail. So, at first i updated the custom lipid name to the desired residue with myristoyl tail. In SCD toolbox, I tried following selections:

**1. Carbon atoms of this residue:
name C11 C12 C13 C14 C10 C9 C8 C7 C6 C5

1. all**

But both of them gave me the following error messages:

Error:
atomselect: cannot parse selection text: name C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 and resname GLYM and index
atomselect: cannot parse selection text: name C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 and resname GLYM and index
while executing
"atomselect top "$sel and index $leafindexes""
(procedure "::membranescd::compute_order" line 31)
invoked from within
"::membranescd::compute_order $CHANNEL $lipids $chains $atomselection $f $nleaf $from"
("uplevel" body line 5)
invoked from within
"uplevel $block"
("while" body line 4)
invoked from within
"while $expression {
set pwvar $f
eval $wrapcmd
uplevel $block
animate delete all
incr f $step
mol addfile $dcd first $f last $f waitfor all
..."
(procedure "::membranetool_common::for_frames" line 19)
invoked from within
"::membranetool_common::for_frames $dcdfile $from $to $step f $wrapcmd {
set progress_text [format "Processing trajectory frame %d (%d%% done). P..."
(procedure "::membranescd::orderPar" line 44)
invoked from within
"::membranescd::orderPar"
(procedure "::membranescd::scd" line 88)
invoked from within

Can i get some help?

[Ismael Rodriguez Espigares]

Dear Shashank Pant,

First, I suggest that you better use the discussion forum, so other people experiencing the same problem can be aided with the resolution of your questions.

Secondly, are you trying to measure the SCD of myristoyl tail attached to a protein residue?
If the answer is afirmative, this is a case that we have not tested and we cannot answer why is failing right know. So, probably is going to take us some time to figure out what went wrong and even if this case is supported by our software.

Best regards,

Ismael.

[Ismael Rodriguez Espigares]

Also, could you provide the command that is printed in the terminal when you run the computation?

Thanks.