Re: VMD/NAMD two identical molecules solvate in a water sphere

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 23 2009 - 12:06:21 CDT

Hi David,
if I misunderstood your question, could you clarify it? The procedure
that I gave you will (with a slight amendment; see below) load the same
molecule twice (and thus give you two identical molecules), offset the
coordinates of one of them, and then generate a psf/pdb that will
simultaneously display both molecules. What else are you trying to do?

# forgot to load psfs for the individual molecules the first time
mol new myfile.psf
mol addfile myfile.pdb
mol new myfile.psf
mol addfile myfile.pdb
set sel [atomselect top all]
$sel moveby {20 0 0 }

(and then use the Merge Structures graphical interface as before)

Peter

David Jiang wrote:
> Hi peter,
>
> Thanks for your help. I think you misunderstood my question. I was
> wondering if there's a way I can create one psf/pdb file that will
> display both the original molecule and the offset molecule. I appreciate
> it.
>
> David
>
> On Tue, Jun 23, 2009 at 11:17 AM, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Hi David,
> what you need to do is combine the two molecules after offsetting the
> coordinates of one of them. So you could, for example, do the following
> (using the command line):
>
> mol new myfile.pdb
> mol new myfile.pdb
> set sel [atomselect top all]
> $sel moveby {20 0 0 }
>
> And then use the graphical interface to combine the two molecules, one
> of which has been moved 20 angstroms along the x axis.
>
> Best,
> Peter
>
> David Jiang wrote:
> > Hi,
> >
> > Is there a way to combine two identical molecules with offset
> > coordinates so that one psf file and one pdb file will display both
> > molecules? I saw that there is a plug-in on VMD 1.8.7 Beta but it
> > overlaps the two molecules. Is there a way to use this plug-in so that
> > it is possible to show both molecules when combined. If not, how can I
> > do this? Thank you for your help.
> >
> > David
> >
> > On Sat, Jun 20, 2009 at 12:21 PM, Joshua Adelman
> <jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>
> > <mailto:jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>>> wrote:
> >
> > Hi David,
> >
> > If both molecules have identical coordinates, then VMD won't
> > separate them automatically. You can translate one of the
> molecules
> > a particular distance using the TCL command line. See:
> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node183.html#14513
> >
> > While it is standard practice to solvate with a shape that
> you can
> > apply periodic boundary conditions to, I imagine that you
> could use
> > the solvate plugin and a little tcl scripting to create a sphere.
> > What you'd want to do is to create a box around your protein
> that is
> > more than generous in size, such that it could contain the sphere
> > that you want. Then you could select atoms that are within some
> > distance (the radius of your sphere) from the center of the
> box (or
> > an atom that is approximately at the
> > center), and write a new PDB just with those atoms.
> Alternatively you could use the script supplied with the NAMD tutorial:
> >
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
> >
> > Best of luck.
> >
> > Josh
> >
> >
> > On Jun 20, 2009, at 9:02 AM, David Jiang wrote:
> >
> >> Hi all,
> >>
> >> My name is David and I am a high school student interning at the
> >> University of Houston. I'm trying to solvate two identical
> >> molecules in a water sphere but I have been unsuccessful for a
> >> number of reasons. I do not know how to make it so that VMD
> >> doesn't overlap the two identical molecules and instead, allows
> >> both molecules to be seen. In addition, is there a way to solvate
> >> this two molecule structure in a water sphere using NAMD? I would
> >> really appreciate any help and thank you all for your time.
> >>
> >> David
> >>
> >
> >
> ------------------------------------------------------------------------------------------------------
> > Joshua L. Adelman
> > Biophysics Graduate Group Lab: 510.643.2159
> > 218 Wellman Hall Fax: 510.642.7428
> > University of California, Berkeley
> > http://nature.berkeley.edu/~jadelman
> <http://nature.berkeley.edu/%7Ejadelman>
> > <http://nature.berkeley.edu/%7Ejadelman>
> > Berkeley, CA 94720 USA jadelman_at_berkeley.edu
> <mailto:jadelman_at_berkeley.edu>
> > <mailto:jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>>
> >
> ------------------------------------------------------------------------------------------------------
> >
> >
> >
> >
>
>

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