From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Mon Oct 17 2011 - 17:46:26 CDT

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
>>
>
>
>