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

From: David Jiang (davidbjiang_at_gmail.com)
Date: Tue Jun 23 2009 - 10:27:07 CDT

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>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>
> Berkeley, CA 94720 USA
jadelman_at_berkeley.edu
>
> ------------------------------------------------------------------------------------------------------
>
>
>
>

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