From: Denilson F. Oliveira (
Date: Fri Dec 02 2016 - 05:51:38 CST

Dear all,

I have found a small problem in both VMD 1.9.2 and 1.9.3:

1) Chlorine atoms in my pdb and str files were named "Cl".

2) These files were used as input for the Autopsf plugin, which
generated the corresponding pdb and psf files without any problem. In
the generated files chlorine atoms were also named "Cl".

3) The pdb and psf generated files were used as input for the Solvate
plugin that converted the coordinates of all chlorine atoms to zero (x=0
, y=0, z=0).

To avoid this problem chlorine atoms must be named "CL" in the original
pdb and str files.

Best wish.


Dr. Denilson F. Oliveira
Professor Titular
Laboratório de Produtos Naturais
Departamento de Química
Universidade Federal de Lavras
Caixa Postal 3037
CEP 37.200-000
Tel: (55) (35) 3829-1623
Fax: (55) (35) 3829-1812