VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 13 2019 - 00:33:24 CST

Hi,
  From your description, it sounds to me like some part(s) of your
structure were partially wrapped in one or both cases, which
could lead to all kinds of trouble later when trying to align the
structures and compute RMSF etc. You should be able to use the
same atom selections you're using for analysis and visually verify
whether what you're computing RMSFs on actually makes sense or not
pre/post wrapping/unwrapping/rewrapping/etc.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 05, 2019 at 09:55:13PM +0530, Adupa Vasista wrote:
> Dear VMD users,
>
> I am having trouble with the RMSF calculations. I am using a script to
> calculate RMSF.
>
> System: Protein solvated in water with Ligands surrounding it.
>
> As my simulation progresses, some chains of the protein came out of the box
> and due to PBC, it entered from the other side. To fix this issue I
> Unwrapped and wrapped the trajectory. The following commands were performed:
>
> 1) pbc unwrap -all -sel "not water" %% To save time I did not unwrap
> water.
> 2) pbc wrap -all -compound fragment -center com -centersel protein
>
> I am getting huge differences in RMSF in Raw (without wrapping) trajectory
> and with wrapping trajectory. Which one should I consider? However, RMSD
> in both cases is the same. Is the alignment of chains is different after
> wrapping?
>
> RMSF script:
> Before sourcing the below script alignment is done through RMSD trajectory
> tool "Align" option
> ##Alignment of alpha carbons with the reference frame##
> proc rmsf_ca {seltext1 seltext2} {
> set ca [atomselect top "$seltext1 and name CA"]
> set rmsf [measure rmsf $ca]
> set outfile [open "${seltext2}.dat" w]
> set count 1
> foreach x $rmsf {
> puts "rmsf of $count is $x"
> #set k [expr $x/10]
> puts $outfile "$count $x"
> incr count
> }
> puts "done"
> close $outfile
> }
>
> Thank You. 

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