VMD-L Mailing List

From: Angelo Rossi (angelo.raymond.rossi_at_gmail.com)
Date: Sat Jul 11 2009 - 13:47:11 CDT

Hello:

I need help with the new version of pbc tools.

Recently, I upgraded to

rossi_at_siduxbox:~/moyle_ibm$
vmd
rlwrap: Command not found.
Info) VMD for LINUXAMD64, version 1.8.7beta5 (June 1,
2009)
Info) http://www.ks.uiuc.edu/Research/vmd/

which also provides pbctools v2.5. Previously, I was using vmd 1.8.6 with
pbctools v 2.4

I am not sure what the error about rlwrap means. Perhaps, it is related to
my problem below.

The behavior is of pbctools v2.5 appears different from that of pbctools
v2.4

I have a solvated protein+lipid bilayersolvated with water.

I load the amber parm7 file ...

vmd > Info) Using plugin parm7 for structure file
/home/rossi/moyle_ibm/wet.top
Info) Analyzing structure ...
Info) Atoms: 557855
Info) Bonds: 557208
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 145445
Info) Waters: 142707

and the coordinates ...

Info) Segments: 1
Info) Fragments: 143718 Protein: 202 Nucleic: 0
File '/home/rossi/moyle_ibm/equil002.coor' appears to be other-endian.
Info) Using plugin namdbin for coordinates from file
/home/rossi/moyle_ibm/equil002.coor
Converting other-endian data from NAMD binary file.
Info) Finished with coordinate file /home/rossi/moyle_ibm/equil002.coor.

Initially, before invoking pbctools, the protein+lipid bilayer is in pieces
at the four corners of a cube.
I want to re-center the protein+lipid bilayer"

package require pbctools
2.5
vmd > ls
equil002.coor equil002.dcd equil002.xsc equil002.xst equil002_xst.dat
moyle2.out20000 wet.top
vmd > pbc readxst equil002.xst
vmd > pbc wrap
Info) 100.0% complete (frame 0)

The protein+bilayer now seems to be centered inside the cube, but the
surrounding water is really in a tangle.
There are bonds to water from one side of the cube to the other.

With pbctools v2.4, the above commands were sufficient, and the structure
and water were wrapped fine.

But now, pbctools v2.5 gives different behavior.

Can someone provide guidance on how to correct this.

Thank you for your attention.

Kind regards,

Angelo