# [gmx-users] dPCA "atoms"

Russell Green russellwgreen at gmail.com
Mon Jun 11 20:45:19 CEST 2007

```Thanks Yang Ye! I will look into this further. Thanks for the program, I'm
sure that will save me much time.

Russell Green

On 6/11/07, Yang Ye <leafyoung at yahoo.com> wrote:
>
>  As what we normally do with dPCA, after obtaining the 2D projection of
> first and second principle, we make it into a 3D plot of free energy
> surface. The awk program is provided below to do such conversion. On this
> surface, we can located regions with low free energy and this leads us to go
> back to 1D projection to locate which frames are inside the regions.
> Clustering or averaging may apply to all the frames found in one region. So,
> in the end, structure are found inside the trajectory for closer inspection.
>
> BEGIN {
>    i=0
>    grid_num=40.0
>
>    x_max=0.0
>    y_max=0.0
>    x_min=0.0
>    y_min=0.0
>
>    temp=300
>    dkt=8.31/1000.0*temp/4.182
> }
>
> {
>    x[i]=\$1
>    y[i]=\$2
>
>    if (\$1>x_max) x_max=\$1
>    if (\$2>y_max) y_max=\$2
>    if (\$1<x_min) x_min=\$1
>    if (\$2<y_min) y_min=\$2
>    i++
> }
>
> END {
>    pt_num=i
>
>    grid_x_size=(x_max-x_min)/grid_num
>    grid_y_size=(y_max-y_min)/grid_num
>
>    dm=0
>    for(i=0;i<pt_num;i++) {
>       grid[(int((x[i]-x_min)/grid_x_size)),
> (int((y[i]-y_min)/grid_y_size))]++
>       g=grid[(int((x[i]-x_min)/grid_x_size)),
> (int((y[i]-y_min)/grid_y_size))]
>       if(dm<g) { dm=g; }
>    }
>
>    mm=0;
>    for(i=0;i<grid_num;i++) {
>       for(j=0;j<grid_num;j++) {
>          if(grid[i,j]!="") { grid[i,j]=dkt*log(dm/grid[i,j]); if
> (grid[i,j]>mm) {mm=grid[i,j];} }
>       }
>    }
>
>    for(i=0;i<grid_num;i++) {
>       for(j=0;j<grid_num;j++) {
>          if(grid[i,j]=="") { grid[i,j]=mm+0.01 }
>          print x_min+(i+0.5)*grid_x_size " " y_min+(j+0.5)*grid_y_size " "
> grid[i,j]
>       }
>    }
> }
>
>  ----- Original Message ----
> From: Russell Green <russellwgreen at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, June 12, 2007 2:17:45 AM
> Subject: [gmx-users] dPCA "atoms"
>
> Dear Gromacs community,
>
>      I've been using the PCA analysis in dihedral space for a chain of my
> protein of interest. I made a script to collect the atom quadruplets
> corresponding to the phi and psi angles and output them to an index file. I
> followed the steps in the paper manual and everything worked as it should;
> however, is there any way to relate the dihedral PCA information to each
> residue that contributed to the analysis? As it stands, my dummy reference
> file contains 715 "atoms" but the analysis was done for about 536 residues
> so that's 3 atoms per residue helping to define the dihedral angles. Could
> someone please provide some suggestions or more insight? I've searched the
> net and the mailing list but have found no information regarding my
> question.
>
> Russell Green
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