VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Wed Nov 13 2019 - 02:40:29 CST

Thank you for the response.

Sorted it out.

On Wed, Nov 13, 2019 at 12:03 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*