VMD-L Mailing List

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Mon Mar 27 2006 - 08:31:20 CST

 Dear All
I meet with a strange question, after I use psfgen and top_all27_prot_na.rtf
file to generate the psf and pdb file of the protein,they are named mol.psf,
mol.pdb, respectively , then I solvate the generated pdb using VMD
version1.84b13(the test version download from BiocoRE), however, the box is
just a rectangle, and the protein is in the one end of the cuboid, but not
locate at the center. The total atom in the whole system is about 47000.

 I use the command: solvate mol.psf mol.pdb -t 8-o mol_sol.

But, at a earlier time, when I use the same psfgen and with
top_all22_prot.inp to generate the psf and pdb file, and then solvate the
pdb using the same VMD with the same command, the box is cube and the
protein is at the center. The total atom in the whole system is about 25000.

Why the box, the protein location and the total atom number are so large? 

--
   Shulin Zhuang
Chemistry Department
Zhejiang University PRC
shulin.zhuang_at_gmail.com