VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Oct 28 2021 - 09:26:11 CDT

Small comment.

Measure RMSD should not be used directly.
To ensure no translation effects are considered, align the molecule first
and then calculate the RMSD.

Unless you have pre-aligned the trajectory - in which case doing the above
will have no effect.

On Thu, Oct 28, 2021 at 10:10 PM Mi Yang <drmiyang2019_at_gmail.com> wrote:

> Dear Natalia,
> Thanks for your comments. We have slightly revised our script in the light
> of your comments, which we were using for the Ligand-Protein complex. It
> worked fine for us now. Please see the attached script in case, if anyone
> else needs it.
> One has to change the range of ligand atoms numbers.
>
> On Thu, Oct 28, 2021 at 2:42 PM Natalia Ostrowska <
> n.ostrowska_at_cent.uw.edu.pl> wrote:
>
>> I made like three mistakes in these commands 😅 I was writing from my
>> phone. You can email me for the correct version later, but this is
>> definitely the kind of script you need
>>
>> On Thu, 28 Oct 2021, 13:33 Natalia Ostrowska, <n.ostrowska_at_cent.uw.edu.pl>
>> wrote:
>>
>>> Hi,
>>> You don't have to run any additional simulations etc
>>> Let me introduce you to the glorious tk console :P :P
>>> let's say you have 1000 frames. type something like
>>> set n 0
>>> set ref atomselect ["your ligand" frame 0]
>>> for {set i 0} {$i<1001} {incr i} {
>>> set conf [atomselect top "your ligand" frame $i]
>>> puts "$i [measure rmsd $ref $conf]" }
>>>
>>> "Your ligand" will be something like "resid X" or "chain Y and resid 23
>>> to 39", have a look at your pdb file, and find how is the ligand called etc
>>> and look for the atomselect commands in the tutorial. I think pdb + dcd
>>> files will work, you don't need PSF for this particular case
>>>
>>> How-to:
>>> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html
>>> https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html
>>>
>>>
>>> On Thu, 28 Oct 2021, 11:50 Mi Yang, <drmiyang2019_at_gmail.com> wrote:
>>>
>>>> Dear Colleagues,
>>>> We have performed MD for RMSD and RMSF calculation of Ligand-protein
>>>> complex using NAMD/VMD. Now, one reviewer is insisting us to also calculate
>>>> RMSD and RMSF of Ligand only.
>>>> Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file
>>>> or through a separate MD?
>>>> I have tried RSMD calculator of VMD after opening the psf,pdb and dcd
>>>> file but "atom selection" is giving error. I wrote UNK and/or LIG ETC. as
>>>> per psf file but none worked..
>>>>
>>>> Many thanks in advance1
>>>> DR.SHABBIR
>>>>
>>>