VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Apr 22 2008 - 07:02:42 CDT

Hi,

I am using a simple script to insert palmitic acid molecules into a popc
lipid bilayer. I make an alignment of my palmitic acid atoms with the
palmitic acid side chain of POPC. After the alignment, however, the
headgroup of palmitic acid always ends up in the interior of the bilayer,
instead of the interface. This does not change if I limit my alignment
selection to the first few atoms near the headgroup. Why is this happening ?
The script is attached. Thank you

-Maria
############

# For POPC, C50 is the terminal methyl carbon on the palmitic acid, and O33
and O35 are the ester oxygens atoms
# For PALM, C1 is the terminal methyl carbon on the palmitic acid, and O1
and O2 are the ester oxygens atoms, linked to the carboxylic acid carbon
atom C16

mol new popc.pdb
mol new palm1.pdb

set c1 [atomselect 0 "resid 76 and (name O33 or name C34 or name O35 or name
C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42
or name C43 or name C44 or name C45 or name C46 or name C47 or name C48 or
name C49 or name C50)"]

set c2 [atomselect 1 "name O1 or name O2 or name C16 or name C15 or name C14
or name C13 or name C12 or name C11 or name C10 or name C9 or name C8 or
name C7 or name C6 or name C5 or name C4 or name C3 or name C2 or name C1)"]

set M [measure fit $c2 $c1]
set all1 [atomselect 1 all]
$all1 move $M
$all1 writepdb palm-moved.pdb
############

The alignment still has the wrong direction if I change the selection to:

set c1 [atomselect 0 "resid 76 and (name O33 or name C34 or name O35 or name
C36 or name C37 or name C38 or name C39) "]
set c2 [atomselect 1 "name O1 or name O2 or name C16 or name C15 or name C14
or name C13 or name C12"]