VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Aug 01 2018 - 10:22:57 CDT

This is not tested. I am writing this on the fly - but something similar if
not the same should work for you...

# define range of residues
# for each residue in range

set fid [open vals.dat a]
set nf [molinfo top get numframes]
set res_in_ref [atomselect top "resid 15"]
for {set i 0} {$i<$nf} {incr i} {

set in_fr_res_sel [atomselect top "resid 15" frame $i]

set mx_ [measure fit $in_fr_res_sel $res_in_ref]

$in_fr_res_sel move $mx_
set rmsd_ [measure rmsd $in_fr_res_sel $res_in_ref]
puts $fid $i\t$rmsd_
$in_fr_res_sel delete

}
$res_in_ref delete
close $fid

The above will compute the rmsd of residue 15 -- you can have this in a
nested loop and iterate the outer loop over all the residues.
The number that will be returned will be the average movement of all atoms
in residue -

However -- YOU should not be doing this. Since you are aligning each
residue optimally (using measure fit) - it not be correct in the context of
the whole structure. Perhaps you could pre-align your trajectory using the
entire structure and then remove the "measure fit" bit ...

Anyway - as I mentioned before I didn't test this script but it should be
relatively straightforward to trouble shoot. Write back if something isn't
clear.

On Wed, Aug 1, 2018 at 10:53 PM Sasthi Charan Mandal <sasthi.phys_at_gmail.com>
wrote:

> Dear Ashar,
> Thanks for your suggestion. I had a doubt about rmsd and rmsf and
> now it is cleared. What I want to calculate is the rmsd of each residue
> over a particular time period and for all frames within that time period.
> But using the above script which I shared does not give the expected
> result. Is anything wrong in the script?
> Thanks
>
> On Wed, Aug 1, 2018 at 2:09 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> Again the same problem.
>>
>> You use
>>
>> [measure rmsd $sela $selb]
>>
>> it should be measure rmsf
>>
>> Secondly - this is not how rmsf is calculated.
>>
>> the simplest way to calculate the RMSF is
>>
>> load your trajectory
>> make 1 selection (just 1) holding your atoms of interest. (eg. roi_atoms)
>>
>> now use
>>
>> measure rmsf $roi_atoms
>>
>> if you use the above command all frames in your trajectory will be used
>> to calculate the rmsf.
>> if you want to limit them as I think you are trying to do (not exactly
>> sure) add frame numbers
>>
>> so
>>
>> measuer rmsf $roi_atoms 50 60
>>
>> with the above command only frame 50 through 60 will be used.
>>
>> keep in mind the difference in math between RMSD and RMSF.
>> RMSD is per frame -- so you get a trend
>> RMSF is per set of frames -- so you will get just 1 value (doesn't matter
>> if you use 50 frames or 5000).
>>
>> check this page for more details:
>>
>> https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html
>>
>>
>> On Wed, Aug 1, 2018 at 4:17 PM Sasthi Charan Mandal <
>> sasthi.phys_at_gmail.com> wrote:
>>
>>> Oh I am sorry. It will be rmsf. So it would be very much helpful for me
>>> if you would provide me the tcl script. I have one script but using this
>>> script I could not get the expected result. Could you please check my
>>> script and let me know what is wrong here?
>>> The script is:
>>> set outDataFile [open rmsf.dat w]
>>> for {set r 491} {$r <= 512} {incr r} {
>>> set sela [atomselect top "resid $r"]
>>> set selb [atomselect top "resid $r"]
>>> $sela frame 0
>>> for {set f 0} {$f<=9990} {incr f} {
>>> $selb frame $f
>>> display update
>>> set val [measure rmsd $sela $selb]
>>> set resid $r
>>> puts $outDataFile "$resid $f $val"
>>> }
>>> }
>>> close $outDataFile
>>> return
>>> }
>>>
>>> On Wed, Aug 1, 2018 at 6:10 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>>
>>>> The subject of the mail is asking for rmsf where as in the email you
>>>> say rmsd. So which one?
>>>>
>>>> Rmsd and rmsf can both be obtained using the "measure" command.
>>>>
>>>> Remember to remove translational and rotational effects from your
>>>> system prior to their use.
>>>>
>>>> Write back if this doesn't help and an example "script" can be provided.
>>>>
>>>> On Aug 1, 2018 00:06, "Sasthi Charan Mandal" <sasthi.phys_at_gmail.com>
>>>> wrote:
>>>>
>>>> I want to calculate the rmsd of each base pair of dna over a specified
>>>> time.. So if anyone have the script I will be thankful to you if you
>>>> provide me.
>>>> Thanks
>>>>
>>>>
>>>>
>>>
>>
>> --
>> Best,
>> /A
>>
>
> 

-- 
Best,
/A