Re: Water molecules inside protein?

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Jun 06 2007 - 12:53:03 CDT

Hi Harisch,

If I understand it right your problem is to center the protein in the
middle of the box so that it is completely surrounded by water. During
dynamics the protein diffuses and it can happen that part of it is outside
of the primary cell. Now you want to put the whole protein into the middle
of the primary cell.

I don't know if there is a way to do that with VMD. However, CHARMM can do
that and also Gromacs. The latter is free. The command looks like this:

trjconv -f snapshot.pdb -s snapshot.pdb -o snapshot_center.pdb -center -pbc inbox

I used it a long time ago, so you should read the gromacs documentation to
understand how it works. I also applied it only to single snapshots but
I'm sure you can do it for the whole trajectory in one shot. However, you
need to convert the dcd trajectory into trr using VMD. Also you need to
make sure that the crystal information is in your dcd file for each frame.

Have you already posted this problem to the VMD list? It could be that
somebody there might know how to do this with VMD.

Good luck,

        Gianluca

On Wed, 6 Jun 2007, hl332_at_drexel.edu wrote:

>
> Hi Steve,

> Thanks for your reply but I am interested in new waters coming in
> and going out from center of my protein. Unwrapping the all things
> is not going to help because water will diffuse away due to
> unwrapping thing. I am not interested in seeing my protein
> stationary, i know it can be done by fit. I dont think so doing
> fitting the way you told is going to show me real waters interacting
> with protein all the time? CORRECT ME in case i misunderstood.
>
> Thanks again
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
> ----- Original Message -----
> From: Stephen Hicks <shicks_at_ccmr.cornell.edu>
> Date: Tuesday, June 5, 2007 10:07 pm
> Subject: Re: namd-l: Water molecules inside protein?
>
> > Harish,
> >
> > I'm not entirely sure I understand what you're asking, but if you're
> > just looking to track the water molecules, then unwrapping boundaries
> > for the entire system should be sufficient. You can use your initial
> > frame as a reference, and then for each successive frame measure the
> > fit back to the reference frame for just the protein and apply that
> > transformation to all molecules, including all the waters. This will
> > make things look like your protein is more or less stationary.
> >
> > -steve
> >
> > On 6/5/07, hl332_at_drexel.edu <hl332_at_drexel.edu> wrote:
> > > Hi All,
> > > I have been doing an NVE run of my protein with periodic
> > boundary conditions and my protein slowly moves during run, goes
> > out and wrapped to another side of box. ALl that is fine. I want to
> > track the water molecules in the center of protein during all
> > frames. I dont know how to tack them when protein itself is moving
> > and wrapped too. I am not sure doing unwrapping only protein or all
> > system can help anyhow? ANy help from experienced users will do great.
> > > THANKS AND REGARDS
> > > HARISH
> > >
> > > -------------------------------------------------
> > > Harish Vashisth (Ph.D Candidate)
> > > CAT-361,Chemical & Biological Engg.
> > > Drexel University, Philadelphia, PA
> > > office: 215-895-5823
> > >
> > >
> >
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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