VMD-L Mailing List
From: Denilson F. Oliveira (denilson_at_dqi.ufla.br)
Date: Fri Dec 02 2016 - 05:51:38 CST
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.
-- Dr. Denilson F. Oliveira Professor Titular Laboratório de Produtos Naturais Departamento de Química Universidade Federal de Lavras Caixa Postal 3037 Lavras-MG-Brasil CEP 37.200-000 Tel: (55) (35) 3829-1623 Fax: (55) (35) 3829-1812 e-mail: denilson_at_dqi.ufla.br