VMD-L Mailing List

From: Nupur Bansal (nupur.b298_at_gmail.com)
Date: Mon Oct 28 2013 - 11:06:07 CDT

Hello All,

I am trying to use namdenergy plugin for computing the non bonded interactions in my protein-ligand system

namdenergy -sel $selL $selP -par /Users/Nupur/CzrA_project/traj/sb_cur1/cur1_sb_strip.prmtop -nonb -ofile try1

where selL and selP are my selections. cur1_sb_strip.prmtop is my parameter file.

But, the namdenergy command gives me an error:

could not locate namd2
please specify the path

When I did not select it, it gave me an error:
couldn't execute " ": no such file or directory

However, it is generating name-temp.dcd, .log, .pdb and .namd files

Can anybody please guide me, what possibly could be wrong with this? I am using Amber12 for simulations and not NAMD.

Thanks
Nupur