AMBER Archive (2007)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Jun 05 2007 - 00:04:34 CDT

> 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_at_O5' :1_at_C5' :1_at_C4' :1_at_C3'
dihedral d0 out dihedrals/d0.dat :1_at_C5' :1_at_C4' :1_at_C3' :1_at_O3'
dihedral c0 out dihedrals/c0.dat :1_at_O4' :1_at_C1' :1_at_N1 :1_at_C2
dihedral cm0 out dihedrals/cm0.dat :1_at_O4' :1_at_C1' :1_at_N1 :1_at_C6

#
# A
#
dihedral e2 out dihedrals/e2.dat :2_at_C4' :2_at_C3' :2_at_O3' :3_at_P
dihedral z2 out dihedrals/z2.dat :2_at_C3' :2_at_O3' :3_at_P :3_at_O5'
dihedral a2 out dihedrals/a2.dat :2_at_O3' :3_at_P :3_at_O5' :3_at_C5'
dihedral b2 out dihedrals/b2.dat :3_at_P :3_at_O5' :3_at_C5' :3_at_C4'
dihedral g2 out dihedrals/g2.dat :3_at_O5' :3_at_C5' :3_at_C4' :3_at_C3'
dihedral d2 out dihedrals/d2.dat :3_at_C5' :3_at_C4' :3_at_C3' :3_at_O3'
dihedral c2 out dihedrals/c2.dat :3_at_O4' :3_at_C1' :3_at_N9 :3_at_C4

pucker p1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out dihedrals/pucker1.dat
pucker p3 :3_at_C1' :3_at_C2' :3_at_C3' :3_at_C4' :3_at_O4' out dihedrals/pucker3.dat
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