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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 23 2009 - 11:17:54 CDT

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>> 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>
> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
> <mailto:jadelman_at_berkeley.edu>
> ------------------------------------------------------------------------------------------------------
>
>
>
>

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