AMBER Archive (2006)

Subject: Re: AMBER: Dihedral analysis

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Jul 03 2006 - 14:47:42 CDT

> I use rdparm and call my parmtop file, and then look at the dihedral angles of
> interest by using printdihedral :@36 to look at the dihedral bonds in amino
> acid 36- in this case leucine. My result is as follows:
>
>
> RDPARM MENU: printdihedral :@36
> Mask [:@36] represents 1 atoms

OK, the nomenclature is ":" for residue and "@" for atom. In this case,
with both present, the ":" is ignored; really what should be returned is
an error here, but what :@36 is being interpreted as is :*@36, i.e. atom
#36 in any residue.

Below for this you will only match 1 atom #36 which is :3_at_HG3 (or residue
three, atom named HG3).

> Dihedral pk phase pn atoms
> 70: 0.150 0.00 3.0 :3_at_HG3 :3_at_CG :3_at_CB :3_at_HB2 (36,34,37,38)
> 71: 0.150 0.00 3.0 :3_at_HG3 :3_at_CG :3_at_CB :3_at_HB3 (36,34,37,39)
> 72: 0.160 0.00 3.0 :3_at_HG3 :3_at_CG :3_at_CB :3_at_CA (36,34,37,40)
> 79: 0.156 0.00 3.0 :3_at_HD3 :3_at_CD :3_at_CG :3_at_HG3 (33,31,34,36)
> 83: 0.156 0.00 3.0 :3_at_HD2 :3_at_CD :3_at_CG :3_at_HG3 (32,31,34,36)
> 89: 0.156 0.00 3.0 :3_at_N :3_at_CD :3_at_CG :3_at_HG3 (30,31,34,36)
...
> RDPARM MENU: printdihedrals :@33
> Mask [:@33] represents 1 atoms

Here you get :3_at_HD3.

What you want is

dihedrals :33
dihedrals :36

This is useful for showing what dihedral torsion terms are actually in
your prmtop file. These may or may not correspond to what torsion angles
you want to measure via ptraj...

Right now, the input to the dihedral monitoring routines in ptraj are
rather clumsy in that you have to specify each angle of interest
independently. I've heard plenty of grumbling on this issue (in that
people would like to say track all phi, all psi and all chi without having
to list EACH one). I personally get around this via perl scripts (for
DNA) set up to automatically create the input I need given a list of
residue names OR I just suck it up and put in the list by hand... For
DNA, I have something like:

#
# G1
#
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_N9 :1_at_C4

#
# C2
#
dihedral e1 out dihedrals/e1.dat :1_at_C4' :1_at_C3' :1_at_O3' :2_at_P
dihedral z1 out dihedrals/z1.dat :1_at_C3' :1_at_O3' :2_at_P :2_at_O5'
dihedral a1 out dihedrals/a1.dat :1_at_O3' :2_at_P :2_at_O5' :2_at_C5'
dihedral b1 out dihedrals/b1.dat :2_at_P :2_at_O5' :2_at_C5' :2_at_C4'
dihedral g1 out dihedrals/g1.dat :2_at_O5' :2_at_C5' :2_at_C4' :2_at_C3'
dihedral d1 out dihedrals/d1.dat :2_at_C5' :2_at_C4' :2_at_C3' :2_at_O3'
dihedral c1 out dihedrals/c1.dat :2_at_O4' :2_at_C1' :2_at_N1 :2_at_C2

analyze statistics all

> 2. I would like, from this output, to identify how the phi psi chi and omega
> angles vary with time, over the courseof my trajectory. If I consider phi
> angles for example then I would look for a N-CA linkage, which exists in aa
> 33:
>
> 77: 0.000 0.00 2.0 :3_at_HD3 :3_at_CD :3_at_N :3_at_CA (33,31,30,40)
>
> but not for aa 36 (both leucines). But logically, this dihedral angle must
> exist in both amino acids... Can someone explain this please?
...
> 3. Another thing I notice is that apparently, the dihedral angle entries for
> the specific amino acids I request are not restricted to the amino acid of

Note that you can monitor ANY dihedral, whether real or virtual via the
specification, for example,

  dihedral res1234 out res1234.dat :1 :2 :3 :4

will calculate the dihedral for the center of mass of residues 1-2-3-4
(i.e. rotation around the bond connecting the center of masses of residues
2 and 3). As such, the monitoring tool is powerful and useful, but I
admit tedious in terms of the required input (which I deal with in a perl
script).

Good luck.

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