From: Siddharth Subramanian (siddhu500_at_gmail.com)
Date: Fri Jun 14 2013 - 04:52:55 CDT

Hi
    I have a query regarding merging structures in vmd. I'm trying to
solvate polymer pva in water . I created t polymer PVA containing about 14
C atoms and wanted to see how it behaves when solvated with water. So I
drew the polymer myself in AVOGADRO software and saved it as pdb file.Then
using the tcl script I created new pdb and psf files containing info about
all the atoms. To solvate, I loaded this molecule in VMD and when I tried
to solvate,an error occured saying, MOLECULE DESTROYED BY FATAL ERROR .
So I was going through VMD MAILING LIST and someone had posted to use
another tcl file to solvate. I used that file, executed in vmd , and that
is when I was able to see overlap of atoms, bonds between oxygen of water
and that of the polymer etc..This was clear when I created lammps data file
where I found Oxygen-oxygen bond type, which is weird , suggesting clearly
OVERLAPPING is happening when I try to merge..
 . I would be pleased if you can help me to solve this problem...by
giving me suggestions on where I'm going wrong!!

I used tcl script from this page to solvate...
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks
Plz help!!
Thanks in advance!!