Re: Qwikmd ABF Question

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jul 05 2018 - 13:16:01 CDT

Hi Kelly,

life would be great if things were that simple. The tutorial shows an
example of how to prepare a protein-membrane system. Charmm-GUI produces,
or can produce, a psf and pdb file of your system, does it not? You can use
these files as a starting point of the tutorial, solvate and add ions and
follow the rest of the steps to prepare your system(s).

Best

João

On Thu, Jul 5, 2018 at 10:48 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Hey Joao, thinks for the link. I just wen through the tutorial for the
> membrane section, and it does mention being able to use other lipids
> besides POPC and POPE. However, it doesn't describe a method for changing
> the POPC to say DMPC. Would the simplest way be to open the POPC membrane
> pdb file generated with the membrane builder plugin in QwikMD, and then use
> Structure Manipulate to change the lipid type? Or is there another way to
> change the POPC to DMPC? Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Thursday, July 5, 2018 7:03:31 AM
> *To:* McGuire, Kelly
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: Qwikmd ABF Question
>
> Hi Kelly,
>
> there is a membrane-protein tutorial that you can follow at
> http://www.ks.uiuc.edu/Training/Tutorials/#memprot. NAMD does not detect
> the axis of the membrane in any simulation. The important step here is to
> define the periodic boundary conditions to ensure that the membrane is
> "infinite", so right at the pbc limits, and you don't get water in the
> hydrophobic region
> ​ of the membrane​
> . All these steps are taken care during the structure preparation in VMD
> ​ ​(see tutorial)
>
> and in the definition of the pbc in the configuration files of NAMD.
> Additional options might be useful such as useConstantRatio
> ​
> .
>
> I hope this helps
>
> Best
>
> João
>
>
> On Wed, Jul 4, 2018 at 7:35 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> Thanks for the reply. In your experience, what is the best way to
> generate a bilayer with lipids that aren't available in QwikMD yet, but
> that NAMD can detect the axis of the membrane, so that I can avoid the
> problems that come from mixing programs like CHARMM GUI with VMD/NAMD?
> Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Wednesday, July 4, 2018 6:25:30 PM
> *To:* McGuire, Kelly
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: Qwikmd ABF Question
>
> Regarding QwikMD and Charmm-Gui, I already comment on that on one of your
> previous questions:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/2032.html
>
> From QwikMD user Guide
>
> - *Minimal Box*: Rotate the system and apply a simple solvent box
> padding distance, instead of the formula described in the "MD/MDFF Protocol
> box" description. The usage of this option should be used carefully and the
> "Buffer" distance should be increased to account system rotation/tumble
> during the simulation (see *VMD solvate plugin
> <http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/>*).
>
> QwikMD is doing what you are asking it to do :)
>
> Best
>
> João
>
> On Wed, Jul 4, 2018 at 6:44 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> I don't suppose there is a way to turn off the rotation after selecting
> the Minimization Box option in QwikMD?
>
>
> I get this in the VMD log after I click prepare in QwikMD:
>
>
> "The system was rotated by 360.0 degrees around Z axis and 350.0 degrees
> around X axis."
>
>
> I don't want it rotated around the x or y axes...
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Wednesday, July 4, 2018 7:08:10 AM
> *To:* namd-l_at_ks.uiuc.edu; McGuire, Kelly
> *Subject:* Re: namd-l: Qwikmd ABF Question
>
> Do you create the bilayer with QwikMD? When creating the bilayer, the
> "Minimal Box" option should be blocked. Is this not the case?
>
> On Wed, Jul 4, 2018 at 2:46 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> Something I haven't observed with QwikMD is occurring. I us QwikMD to set
> up the multiple windows I need for my ABF simulation. I create 16 windows
> where my ligand goes from bulk water on the N-terminus of my bilayer
> embedded protein, through the protein, and to the C-terminus bulk water.
> When I use QwikMD to create the solvated bilayer/protein/ligand system on
> the N-terminus side in bulk water (about 15 angstroms from the
> bilayer/protein), my bilayer/protein remains perpendicular to the z-axis,
> which is what I want. My reaction coordinate is along the z-coordinate.
> However, when I do this at the C-terminus bulk water side (about 15
> angstroms into bulk water), QwikMD flips my bilayer/protein/ligand system
> to be perpendicular to the y-axis. This, I assume, creates problems with
> calculating a PMF when all of my other windows are perpendicular to the
> z-axis...I do select Minimal Box and 12 angstrom buffer for all of my
> windows. Why would QwikMD flip my system like this on the C-terminus bulk
> water end but not the other end?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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