VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 27 2008 - 16:35:37 CDT

Try using a smaller subset of atoms to do your alignment and
see if you can get a successful alignment. By excluding any that
may have wrapped over a periodic boundary, you may get a decent
transformation matrix, and then you'd be able to apply it to
all of the atoms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 27, 2008 at 03:01:21PM -0400, Jianhui Tian wrote:
> Hi,
>
> Can anyone give any suggestions? Thanks.
>
> Jianhui
>
> On Fri, Oct 24, 2008 at 6:02 PM, Jianhui Tian <jianhuitian_at_gmail.com> wrote:
>
> > Hi,
> >
> > I found out there was one post regarding this problem before. From my
> > understanding, that problem was because of the peptide cross the boundary of
> > the unit cell.
> > In my calculation, I don't encounter such situation.
> >
> > What I did was:
> > I wrote a script to calculate the RMSD between every two frames of a
> > trajectory for a peptide.
> > The peptide was located in the center of the box for the most of time and
> > its configuration was fluctuating (not really folding/unfolding).
> > And I got warning as following:
> > Matrix: Warning: no convergence (0.00001000<505.03359985 after 1000
> > iterations).
> > Matrix: Warning: no convergence (0.00001000<434.05392456 after 1000
> > iterations).
> > Matrix: Warning: no convergence (0.00001000<484.80929565 after 1000
> > iterations).
> >
> > I am also including my little script here. Thanks in advance.
> > # This code is used to calculated "mean square displacement" of protein.
> >
> > set dcdFile2 ../a8an_rm14_min3.dcd
> >
> > mol new
> > /.automount/polaris/home/tianj/tianj/selfassemble_rmakUA_080429/aklocation/a8an_rm14.prmtop
> >
> > type parm7 first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
> > mol addfile $dcdFile2 type dcd first 0 last -1 step 1 filebonds 1 autobonds
> > 1 waitfor all
> >
> > set num_frames [molinfo top get numframes]
> >
> > set sel1 [atomselect top "protein and backbone"]
> > set sel2 [atomselect top "protein and backbone"]
> >
> > set file2 [open "temp" "w"]
> > set file1 [open "rmsd_t" "w"]
> > # R(t)^2=1/(trun-t)*sum_(trun-t){[x(td+t)-x(td)]^2}
> > # Loop through t.
> > for {set deltai 1} {$deltai < $num_frames} {incr deltai} {
> > # Loop through td.
> > set totmsd 0
> > set totrmsd 0
> > set sumframes [expr $num_frames -$deltai]
> > for {set i 1} {$i < $sumframes} {incr i} {
> > set j [expr $i + $deltai]
> > $sel1 frame $i
> > $sel2 frame $j
> >
> > #compute the transformation
> > set trans_mat [measure fit $sel2 $sel1]
> > #do the alignment
> > $sel2 move $trans_mat
> > set trmsd [measure rmsd $sel1 $sel2]
> > set totmsd [expr $totmsd + $trmsd * $trmsd]
> > set totrmsd [expr $totrmsd + $trmsd]
> > puts $file1 [list $i $trmsd]
> > }
> > set msd [expr $totmsd/$sumframes]
> > set rmsd [expr $totrmsd/$sumframes]
> > puts $file2 [list $deltai $msd $rmsd]
> > }
> >
> > exit
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078