Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions...

From: Thomas Cheatham <>
Date: Mon, 4 Jun 2007 23:04:34 -0600 (Mountain Daylight Time)

> I am performing molecular dynamics simulations of DNA fragments ( with AMBER9).
> I want to analyse several parameters of the nucleic acid during the simulation
> such :
> - the average backbone torsions

You can do this with ptraj, although it is not automagic yet...

> - the average base pair parameters
> - the average pair step parameters

For this I tend to use Curves or 3DNA on individual PDB files.

> - the average puckers

ptraj can do this.

An example input:

# C
dihedral g0 out dihedrals/g0.dat :1.O5' :1.C5' :1.C4' :1.C3'
dihedral d0 out dihedrals/d0.dat :1.C5' :1.C4' :1.C3' :1.O3'
dihedral c0 out dihedrals/c0.dat :1.O4' :1.C1' :1.N1 :1.C2
dihedral cm0 out dihedrals/cm0.dat :1.O4' :1.C1' :1.N1 :1.C6

# A
dihedral e2 out dihedrals/e2.dat :2.C4' :2.C3' :2.O3' :3.P
dihedral z2 out dihedrals/z2.dat :2.C3' :2.O3' :3.P :3.O5'
dihedral a2 out dihedrals/a2.dat :2.O3' :3.P :3.O5' :3.C5'
dihedral b2 out dihedrals/b2.dat :3.P :3.O5' :3.C5' :3.C4'
dihedral g2 out dihedrals/g2.dat :3.O5' :3.C5' :3.C4' :3.C3'
dihedral d2 out dihedrals/d2.dat :3.C5' :3.C4' :3.C3' :3.O3'
dihedral c2 out dihedrals/c2.dat :3.O4' :3.C1' :3.N9 :3.C4

pucker p1 :1.C1' :1.C2' :1.C3' :1.C4' :1.O4' out dihedrals/pucker1.dat
pucker p3 :3.C1' :3.C2' :3.C3' :3.C4' :3.O4' out dihedrals/pucker3.dat
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Received on Wed Jun 06 2007 - 06:07:26 PDT
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