From: Vermaas, Joshua (
Date: Wed Mar 14 2018 - 12:00:01 CDT

Hi Rahul,

My money is on incorrect .psf and .pdb file names relative to your actual protein file names, since right now I'm betting that there is an error in loading the files (the underscores are important in the tutorial!). Then all of your selections will be empty, which will lead to no "bad lipids" being removed. However, I think it might behoove you to check MemProtMD or the OPM database to see if there is a better orientation for your membrane protein. For symmetric channels like KcsA, alignment with the z-axis isn't a bad approximation, but if your receptor isn't symmetric, the approach in the tutorial is not ideal. You also may want to try CHARMM-GUI for assembling the system, which has a relatively intuitive interface for selecting mixed lipid types.


On 03/14/2018 10:47 AM, RAHUL SURESH wrote:
Dear all, I am constructing me POPC-receptor protein complex using VMD, following the following tutorial.>

initially the protein was aligned horizontaly to the lipid bilayer. I used transazix command along various axis to make the protein align perpendicular to the bilayer.

In the section, 2.3 Combination of Membrane and Protein, following the order if commands

mol delete all
mol new kcsa popc raw.psf
mol addfile kcsa popc raw.pdb
set POPC "resname POPC"
set all [atomselect top all]
$all set beta 0
set seltext1 "$POPC and same residue as \ (name P1 and z>0 and abs(x)<15 and abs(y)<15)"
set seltext2 "$POPC and same residue as \ (name P1 and z<0 and abs(x)<10 and abs(y)<10)"
set seltext3 "$POPC and same residue as (within 0.6 of protein)"
set sel1 [atomselect top $seltext1]
set sel2 [atomselect top $seltext2]
set sel3 [atomselect top $seltext3]
$sel1 set beta 1
$sel2 set beta 1
$sel3 set beta 1
set badlipid [atomselect top "name P1 and beta > 0"]
set seglistlipid [$badlipid get segid]
set reslistlipid [$badlipid get resid]

For the last two commands, I found none of the badlipid was selected and named.

Main< (NAMD work-trail-2) 135 % set seglistlipid [$badlipid get segid]
Main< (NAMD work-trail-2) 136 % set reslistlipid [$badlipid get resid]

What should be the cause for this and what can be done?

Thank you

Rahul Suresh
Research Scholar
Bharathiar University