VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 04 2007 - 11:20:30 CDT

Hi Phillip,
my guess would be that the reason that you get only one unit cell if you
coerce everything into one chain is that you end up with repeated
resids; every residue in a chain needs a unique residue id.

I also need to ask, how are the bonds defined in your topology file? In
particular, how are you defining the bonds between unit cells? You're
dealing with a fairly atypical case here, so you may want to drop down
to using psfgen and see if you can build the structure you want there,
since autopsf is intended primarily for biomolecules and may make some
guesses that are inappropriate to your case. If you do this and let me
know what is needed to make it work, I can see about changing autopsf to
recognize such cases.

Peter

Philipp Schoen1 wrote:
> 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