Re: [AMBER] error with NMA calculation

From: Jason Swails <>
Date: Wed, 18 Nov 2015 21:51:45 -0500

On Wed, Nov 18, 2015 at 6:38 PM, Mohammad Salem <>

> Thanks professor. I will try it in serial and see…
> The system is 226 amino acids in a cage of solvent. For doing it “by
> hand”, can you give me suggestions for where the procedure is explained?

​The description is pretty simple. Normal modes are calculated from the
Hessian computed from a local minimum. So the steps are:

1. Minimize each snapshot, making sure to get very close to a local minimum
(it needs to be a lot closer to a local minimum than what you typically do
to prepare for MD). uses the xmin minimizer (this is described
in the manual).

2. Use a nab program to compute the Hessian and, from that, the normal

You can do both of the above two steps in a single nab program (see inside $AMBERHOME/AmberTools/src/mmpbsa_py for an


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Nov 18 2015 - 19:00:04 PST
Custom Search