Hi Ajay,

You can use Bio3D (free software) for normal mode analysis.

Please check below link:

http://thegrantlab.org/bio3d_v2/tutorials/normal-mode-analysis

I would recommend ProDy. Prody interface is included with VMD under the Extensions > Analysis > Normal Mode Wizard > ProDy Interface. Moreover, VMD can read almost any trajectory.

Here are some examples of normal mode analysis using ProDy:

Article Dynamical Flexibility Modulates Catalytic Activity of a Ther...

Preprint Essential Loop Dynamics Modulates Catalytic Activity in α-Chymotrypsin

For more on ProDy, visit http://prody.csb.pitt.edu/

If you are confident with GROMACS, you can also use it for NMA:

http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Normal_Mode_Analysis#:~:text=Resources-,Normal%20procedure%20with%20GROMACS,calculation%20of%20a%20Hessian%20matrix.

You can use Dynamut and Bio3D for normal mode analysis.

Please follow the links.

http://biosig.unimelb.edu.au/dynamut/

https://www.researchgate.net/deref/http%3A%2F%2Fthegrantlab.org%2Fbio3d_v2%2Ftutorials%2Fnormal-mode-analysis

Uttam Pal

Respected Sir,

ProDy interface present in VMD is giving error. Please help me to solve this error.

/home/pps/Desktop/softwares/ProDy-2.4.1/scripts/prody.bat: 1: %~dp0..python: not found

/home/pps/Desktop/softwares/ProDy-2.4.1/scripts/prody.bat: 1: %~dp0..python: not found

while executing

"exec $::NMWiz::pybin $::NMWiz::prody anm --quiet -s $selstr {*}$args "$pdbfn""

(procedure "::NMWiz::prodySubmitANMjob" line 42)

invoked from within

"::NMWiz::prodySubmitANMjob"

(procedure "::NMWiz::prodySubmitJob" line 22)

invoked from within

"::NMWiz::prodySubmitJob"

invoked from within

".nmwizprody.submitFrame.prodySubmit invoke"

("uplevel" body line 1)

invoked from within

"uplevel #0 [list $w invoke]"

(procedure "tk::ButtonUp" line 22)

invoked from within

"tk::ButtonUp .nmwizprody.submitFrame.prodySubmit"

(command bound to event)

Praval Pratap Singh Try to set PYTHONHOME or PYTHONPATH environment variables in the .vmdrc file. Here's how to do this: https://www.ks.uiuc.edu/Research/vmd/current/ug/node162.html

You can get the system python path using the "which" command

$ which python3

Also try to install prody from the repository using

$ sudo apt install python3-prody