Steered NAMD using AMBER Forcefield [Config File]

From: Zeinab Emami (
Date: Sun Jan 18 2015 - 10:07:51 CST

Dear All,

I intend to run Steered Molecular Dynamics for my system consisting of a
protein and a non-standard compound. I parametrized the ligand in AmberTool
and got the files inpdrc and prmtop. I got the pdb file corresponding
inpcrd file which will be modified [for fixed and pulled atoms]. Then, I
noticed that I should add these lines to the config file:

amber on # Specify this is AMBER force field
parmfile prmtop # Input PARM file
ambercoor inpcrd # Input coordinate file

My question is that, should I comment out this lines in

Adjustable Parameter section?

structure mypsf.psf
coordinates mypdb.pdb

Best Regards,

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