problem with solvating a structure

From: Hadi Rahmaninejad (
Date: Tue Feb 26 2019 - 14:32:28 CST

Hello Dear NAMD users,

I am using psfgen in VMD TkConsole in order to solvate a silica structure
containing mostly Si and O atoms with water. The command I am using are:
"solvate silica.psf silica.pdb -t 10"
However, the result is a pdb file in which the coordinate of most of Si and
O is "zero" (0.000). and so the vmd shows a weird structure of one Si
connected to few oxygen and Hydrogen surrounded by water molecules. I
highly appreciate if anybody can help me with this.

Thank you in advance,

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