VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Apr 11 2005 - 16:08:26 CDT

Hi,
First, to build a water shell around an atom (or a group of atoms) you
need both pdb and psf files of your system. In this case, you can build
your pdb and psf files of a K ion by using psfgen. For one atom it is
really straightforward.
After that, you can add the water shell around your ion using the
following line in vmd (in the command line, assuming that the psf and
pdb files you're creating have the name "potassium.psf" and
"potassium.pdb", and that they are in your VMD working directory)

solvate potassium.psf potassium.pdb -o potassium-solvated -s WT -b 2.5
-t 10

-o option is the output name (it will create potassium-solvated.psf and
potassium-solvated.pdb)

-b is the boundary between your ion and the solvent (in Angstroms)
-t is the thickness of the water shell (in this case, using this
example, it'll be the "margin" between the ion and the boundary of the
shell, in Angstroms).

I hope it helps! Please make me know if you have further questions :)
Peace,
Michel

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of M SH
Sent: Monday, April 11, 2005 2:50 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: how to creat a file containing only one potassium ion

maybe this is a too simple question to an expert to answer. But I really

feel frustrated after hours of trials.

I create a pdb file by hand as following,

ATOM 1 K POT 1 1.000 1.770 1.000
END

Or

ATOM 1 POT POT 1 1.000 1.770 1.000
END

then I read it and use writepdb in tcl console through vmd as the
tutorial
says.

then I tried to dissolve it into the water. But I just failed. Thanks

Life is beautiful.