Re: [AMBER] 【amber】center of mass&umbrella sampling

From: Jason Swails <>
Date: Fri, 6 Jun 2014 08:20:20 -0400

On Fri, Jun 6, 2014 at 3:11 AM, whb <> wrote:

> Dear amber users:
> I want to know that the dimer-to-monomer transition of a protein
> by
> using CPHMD simulations and the umbrella sampling method to obtain the
> potential of mean force(PMF) as a function of the distance between the
> centers of mass of the two monomers.
> Now I have a little trouble writing the DISANG file. Monomer has 79AAs. I
> don’t know how to acquire the original distance between the two monomers,
> and don’t know how to define the distance between two residues. I tried to
> read the manual, but still got a little problems. I hope someone could help
> me finish the DISANG file. And tell me how to define the variable number.
> &rst
> iat=-1,-1,
> r1=0.0, r2=10.0, r3=10.0, r4=100.0,
> rk2 =1.0, rk3 = 1,
> iresid=1,
> ​​
> igr1=1-79,

​You cannot specify an atom range in a Fortran namelist. You must specify
each atom your want in your group explicitly. To avoid adding a full 79
atoms to each group, see if you can select a subset that will still give
you basically the same center of geometry.

Other than these errors that were easy to detect, it's impossible to
provide help when we don't know what you did, what error you got, or what
you mean by "define the variable number". Please try and be specific and
report exactly what you tried and the messages you got (do _not_ paraphrase
or summarize).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jun 06 2014 - 05:30:03 PDT
Custom Search