VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Wed Mar 14 2018 - 10:54:23 CDT

Dear all, I am constructing me POPC-receptor protein complex using VMD,
following the following tutorial.

http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf

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 

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*