Re: [AMBER] How to calculate the tilt angle of TM helix

From: Prajwal Nandekar <>
Date: Sat, 10 Aug 2019 10:26:17 +0530

Thanks Callum for the information.
Hi Maria,
TM helix angle can also be calculated using VMD. Please find the script
below, if it helps.

##########CALCULATE Angle of TM helix of Protein ######
set output_TM [open "Protein_TM_angle.dat" w]
mol new protein.pdb
mol addfile trajectory.xtc type xtc waitfor all
set numframes [molinfo 0 get numframes]
for {set frame 0} {$frame < $numframes} {incr frame} {
set p_TM1 [atomselect 0 "protein and resid 6 to 10" frame $frame]
set c_TM1 [measure center $p_TM1 weight mass]
set p_TM2 [atomselect 0 "protein and resid 23 to 25" frame $frame]
set c_TM2 [measure center $p_TM2 weight mass]
set ax_TM [vecsub $c_TM2 $c_TM1]
set lax_TM [veclength $ax_TM]
set k "0 0 1"
set dot_TM [vecdot $ax_TM $k]
set cos_TM [expr "$dot_TM / $lax_TM"]
set ang_rad_TM [tcl::mathfunc::acos "$cos_TM"]
set ang_deg_TM [expr "57.2957795 * $ang_rad_TM"]
puts $output_TM "$frame $ang_deg_TM"
$p_TM1 delete
$p_TM2 delete

Also, please find the attachment of script.
Command to run: vmd -e calc_TM_angle.vmd -dispdev none.
Thanks and best regards,
Prajwal P. Nandekar, Ph.D. (Pharmacoinformatics)
Scientist, Schrodinger Inc. Bangalore
Mobile: +91-9872507189

On Sat, Aug 10, 2019 at 2:20 AM Dickson, Callum <>

> Hi Maria,
> You can use cpptraj and the vector command with type "principal" to get
> the principal axes of inertia of your helix.
> Best,
> Callum
> -----Original Message-----
> From: Maria Bzówka <>
> Sent: Friday, August 9, 2019 4:18 AM
> To: AMBER Mailing List <>
> Subject: [AMBER] How to calculate the tilt angle of TM helix
> Dear All,
> During the simulation I can see quite a lot of changes in the position of
> my TM helix immersed in the lipid bilayer, so I would like to calculate the
> tilt angle between the transmembrane helix principal axis and the vector
> along the Z-axis. However, I'm not so sure how to do that...
> As a principal axis of TM helix I mean the C-alpha atoms from the helix
> (which is 30 residues) and I suppose that I should somehow use the vector
> command from cpptraj?
> Do you have any suggestions?
> Thank you in advance
> Maria
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Received on Fri Aug 09 2019 - 22:00:02 PDT
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