VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jan 10 2018 - 12:31:02 CST

Yes. :) Usually it helps to have the topology file open when doing this. It is by far the most foolproof way of doing this. If you are comfortable with regular expressions (http://www.ks.uiuc.edu/Research/vmd/current/ug/node94.html), the lists can be made easier to type. The groups would become:

name N "C1[1-5]" "H1[1-5]." P "O1[1-4]" #Headgroup only
name "C[1-3]" "H." "C[2-3]1" "O[2-3][1-2]" #glycerol + carbonyl
name "H.*[R-Z]" "C[2-3][2-9]" "C[2-3]1." #Acyl chain

Although in Tcl scripts, the braces and double quotes need to be escaped so that the interpreter doesn't think they are a command. Ex:

set sel [atomselect top "name \"H.*\[R-Z\]\" \"C\[2-3\]\[2-9\]\" \"C\[2-3\]1.\""]

-Josh

On 01/10/2018 10:16 AM, Chitrak Gupta wrote:
Hi Robert,

I usually select headgroup atoms by manually specifying the atom names. It is going to be a long list, but does the job.

Hope this helps,
Chitrak.

On Wed, Jan 10, 2018 at 9:20 AM, Robert Nairn <rn33_at_st-andrews.ac.uk<mailto:rn33_at_st-andrews.ac.uk>> wrote:
Hi all,

I am trying to work out how to calculate contact of the acyl chain and the headgroup of a DMPC lipid within 5 Anstom of a protein residue.

I have previously tried using 'Lipid within 5 of Protein' but I cannot get the separation between the headgroups and acyl chains present.

All the best,

Robert