VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Dec 14 2009 - 17:07:38 CST

Hi, i have som doubts about solvating with water diferent regions in VMD.
Well, i have a pdb file that contains Colunms of atoms of Hydrogen side by
side. They're fixed and there's no bonds. But i only have the pdb file, not
the psf. So I wanted to add water to the left side and the right side of
those columns. I tryed going in the "extensions" and "add solvation box",
but there i could see only one region to add the water... So i tryed
putting only in the right side. I gave the x,y, and z min and max and it
created a "solvate.pdb" and a "solvate.psf". But on those files there were
only the coordinates of the water, and nothing about the colums of hydrogen.
I thought that in this "solvate.pdb" and "solvate.psf" would contain the
whole system. But it didn't. What would it be? Would it be because i don't
have the psf of the columns of hydrogen? And how do i solvate two diferent
regions? Thanks a lot.

Ranyere Deyler Trindade
Unicamp
Brasil
Departamento de Física Aplicada