VMD-L Mailing List

From: Philipp Schoen1 (SCH_at_zurich.ibm.com)
Date: Wed Apr 04 2007 - 09:49:10 CDT

Dear all,
I want to generate a silica surface by using the psfgen tool to get the
corresponding psf to my pdb file which looks like this

HEADER PROTEIN
COMPND Patch4.pdb
AUTHOR GENERATED BY BABEL 1.6
ATOM 1 SI1 Q011 1 4.118 4.481 -12.830 1.00 0.00 Q1
ATOM 2 SI2 Q011 1 0.121 3.053 -9.489 1.00 0.00 Q1
ATOM 3 SI3 Q011 1 3.423 1.626 -6.147 1.00 0.00 Q1
ATOM 4 SI4 Q011 1 6.726 0.198 -2.806 1.00 0.00 Q1
ATOM 5 O5 Q011 1 3.980 2.880 -12.662 1.00 0.00 Q1
ATOM 6 O6 Q011 1 -0.018 1.453 -9.320 1.00 0.00 Q1
....

The Q's denote the unit cell having 40 atoms in it, i.e. Q1 = unit cell
one, Q2 = unit cell 2, ..., Qn = nth unit cell.
My problem: if I use the AutoPSF tool to write the psf file I get n=40
chains which are not connected! Deleting the last column from my pdb file,
i.e. deleting all the Q's results in a psf file which contains only a
single unit cell.
What do I need to do get all the bonds between unit cells in the psf file
(VMD loads it correctly showing all bonds)?

Thank you in advance
Cheers
Philipp