From: Sasthi Charan Mandal (sasthi.phys_at_gmail.com)
Date: Wed Aug 01 2018 - 09:53:16 CDT

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
>