VMD-L Mailing List

From: Javier Goicochea (goicox_at_gmail.com)
Date: Thu Jan 15 2009 - 10:11:05 CST

Hi Christopher,

Thank you for your prompt reply. I tried your script and worked. The only
modification I did, was to change "Quartz" by the name of my PDB file
(MB_PDB01.pdb). Unfortunately, the new PDB and PSF files have more atoms
than my original PDB file. The new number of atoms is a multiple of 9. All
new atoms are created at 0,0,0, so I guess writepsf also follows the
information in the TOP file.

In my case, I was using the following script to create the PSF file (without
calling guesscoord):

psfcontext reset
topology MB_PDB01.pdb.inp
segment X147 {pdb MB_PDB01.pdb}
writepsf MB_PDB01.pdb.psf

X147 is just a dummy name.

Regards, Javier