VMD-L Mailing List

From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Mon Oct 17 2011 - 18:46:35 CDT

Hi Elia,

Thank you for your help! I have been driving myself nuts with all the options
that are available for pbc tools and lack of good examples to guide me.

The command you suggested wraps it nearly perfect, but I get one
artifact in the
last few frames of the trajectory. A 10A slice of the water migrates away from
the rest of the box in one direction and another 3A slice wanders off in
another direction. Is there any way of keeping the water box intact throughout
the trajectory with having these artifacts arise?

Thank you for your valuable help!

Best,
Markus

Quoting "Zumot, Elia Nabil" <enz1_at_pitt.edu>:

> Hi Markus,
>
> I had a lot of trouble myself with the so-called tutorial.
>
> Try this command:
> pbc wrap -centersel "protein" -center com -compound residue -all
>
> This should keep the center of mass of the protein in the center and
> wrap everything else (based on 'residue' around it).
>
>
>
>
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 648 7785 - Fax: 412 648 3163
> enz1_at_pitt.edu
> ________________________________________
> From: Markus K. Dahlgren [markus.dahlgren_at_yale.edu]
> Sent: Monday, October 17, 2011 6:46 PM
> To: Zumot, Elia Nabil
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: centering problem in trajectory tool
>
> My protein drifts during the MD simulation and after a while crosses the
> periodic boundary box. The first frame has the protein centered inside
> the box,
> surround by TIP3P water molecules.
>
> These are the commands I have tried, and everything I have tried results in
> lines being drawn all over the box. I sometimes get an ok trajectory for the
> protein and the ligand, but I want to have the waters wrapped around the
> protein so I can visually inspect water-ligand interactions.
>
> package require pbctools
> set cell [pbc get -now]
> pbc set {90 90 90} -first now -all
> pbc wrap -first now -all -center origin -centersel centerofmass
>
> I have also tried unwrapping it after I get the lines drawn all over the box.
>
> pbc unwrap -first now -all
>
> I have also tried wrapping and unwrapping , including the options:
> -sel "resname UNK"
> -sel "protein"
>
> Basically nothing I have tried gives me the protein centered with
> waters wrapped
> around it. Often the waters are not displayed for over 50% of the
> protein that
> has moved into another periodic boundary box.
>
> ~Markus
>
> Quoting "Zumot, Elia Nabil" <enz1_at_pitt.edu>:
>
>>
>> You need to use the 'wrap' command to wrap everything (or just the
>> ligand) around your protein.
>> You will need to specify the protein selection with the -centersel
>> command to keep your protein in the center of the box.
>>
>> Regards
>>
>>
>> Elia Zomot, PhD
>> Computational and Systems Biology Department
>> School of Medicine, University of Pittsburgh
>> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>> Voice: 412 648 7785 - Fax: 412 648 3163
>> enz1_at_pitt.edu
>> ________________________________________
>> From: Markus K. Dahlgren [markus.dahlgren_at_yale.edu]
>> Sent: Monday, October 10, 2011 4:09 PM
>> To: Zumot, Elia Nabil
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: RE: vmd-l: centering problem in trajectory tool
>>
>> Hi Elia,
>>
>> Yes I tried using pbc unwrap, but that does not solve the problem. I ran pbc
>> unwrap with the following command:
>>
>> pbc unwrap -first now -all
>>
>> I then ran the RMSD trajectory tool. Out of 40ns simulation, the
>> ligand is not
>> placed inside the protein for 10ns. This is an alignment problem that I have
>> not been able to fix with either pbc unwrap or the trajectory tool.
>> If I have
>> the selection: resname UNK in trajectory tool, then the
>> ligand-protein complex
>> is centered and aligned, but the protein is rotationg around the
>> ligand as the
>> trajectory proceeds. Ideally I would have the protein centered and
>> aligned with
>> the ligand so that the protein structure is constantly centered.
>>
>> Any tips on how to do this would be greatly appreciated.
>>
>> Best,
>> Markus
>>
>>
>>
>> Quoting "Zumot, Elia Nabil" <enz1_at_pitt.edu>:
>>
>>> Hi Markus,
>>>
>>> Have you checked the pbc wrap options in VMD?
>>>
>>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>>
>>>
>>>
>>> Elia Zomot, PhD
>>> Computational and Systems Biology Department
>>> School of Medicine, University of Pittsburgh
>>> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>>> Voice: 412 648 7785 - Fax: 412 648 3163
>>> enz1_at_pitt.edu
>>> ________________________________________
>>> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
>>> Markus K. Dahlgren [markus.dahlgren_at_yale.edu]
>>> Sent: Monday, October 10, 2011 9:59 AM
>>> To: vmd-l_at_ks.uiuc.edu
>>> Subject: vmd-l: centering problem in trajectory tool
>>>
>>> Hi,
>>>
>>> I have modeled a protein-ligand complex with explicit waters and during the
>>> simulation there is center of mass movement. The complex was
>>> simulated using
>>> NAMD.
>>>
>>> When I align the complex with the protein selection in the
>>> trajectory tool in
>>> vmd, the ligand is not centered/aligned with the protien for about
>>> 40% of the
>>> trajectory. If I align the complex with the resname UNK selection (ligand
>>> residue name), the trajectory becomes very painful to look at as
>>> the protein
>>> keeps rapidly moving around the centered ligand.
>>>
>>> The ligand is fairly large and has a 10-unit peg linker, which likely
>>> causes the
>>> alignment problem when the linker part of the ligand crosses into the next
>>> periodic boundary box.
>>>
>>> What can I do to center and align the ligand-protein complex so that
>>> I can view
>>> it in VMD?
>>>
>>> Any help would be greatly appreciated!
>>>
>>> Markus
>>>
>>
>>
>>
>
>