VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 27 2006 - 09:41:24 CST

Dear Shulin,
if you just look at the protein generated in your two cases, are there
any differences?
Peter

Shulin Zhuang wrote:

> 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 <mailto:shulin.zhuang_at_gmail.com>