[AMBER] phi-psi distribution

From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 8 Aug 2016 20:54:24 +0000


I am planning to do reweighing for aMD.

The amber tutorial says to generate phi-psi distribution

To reweight a 2D distribution, like our PCA plot or a common Phi-Psi distribution, a file containing the 2D information for each frame has to be generated. For a Phi_Psi distribution file, AmberTools can be used. For example, for dipeptide alanine phi-psi distribution:

# 2 ALA PHI: (1 ACE C)-(2 ALA N)-(2 ALA CA)-(2 ALA C) -180 -180

# dihedral iat 5, 7, 9, 15,

dihedral phi :1.C :2.N :2.CA :2.C out Phi_Psi

# 2 ALA PSI: (2 ALA N)-(2 ALA CA)-(2 ALA C)-(3 NME N) -180 -180

# dihedral iat 7, 9, 15, 17

dihedral psi :2.N :2.CA :2.C :3.N out Phi_Psi


Here it is only for one aminoacid, can anyone tell me how to use it to generate phi-psi for entire protein.

Thanking you,


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Received on Mon Aug 08 2016 - 14:00:02 PDT
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