VMD-L Mailing List

From: Sasthi Charan Mandal (sasthi.phys_at_gmail.com)
Date: Wed Aug 29 2018 - 11:45:47 CDT

Thank you Mr. Ashar. Your script is working fine. A lot of thanks to you.

On Thu, Aug 2, 2018 at 10:47 AM Sasthi Charan Mandal <sasthi.phys_at_gmail.com>
wrote:

> Thank you Ashar for providing the script. I will try and let you know.
>
> On Wed, Aug 1, 2018 at 8:52 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> 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
>>
>
>