obtaining cellBasisVectors from SCALE entries in the PDB file

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Fri Aug 23 2013 - 10:31:28 CDT

• Next message: Vibhor Agrawal: "Implementation of ELASTIC NETWORK model in NAMD"
• Previous message: Norman Geist: "AW: questions regarding the source code in NAMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear NAMD users,

I'm about to start my first simulation with a non-cubic box and I wanted to
make sure that I'm doing things right when setting up the cellBasisVector
entries in the NAMD configuration file.

My PBD file has these CRYST and SCALE entries:

CRYST1 12.5159 12.5159 13.1140 90.00 90.00 120.00 H-3
SCALE1 0.079899 0.046129 0.000000 0.000000
SCALE2 0.000000 0.092259 0.000000 0.000000
SCALE3 0.000000 0.000000 0.076254 0.000000

As I understand, the SCALE entries define the transformation from the
orthonormal basis set to the unit cell basis set. Thus, I inverted this
matrix:

[[ 12.5158012 -6.25783277 0. ]
 [ 0. 10.83905093 0. ]
 [ 0. 0. 13.11406615]]

By comparing the columns of this matrix and the CRYST1 entry in the
pdb, it would seem that the columns
correspond to the cellBasisVector entries for NAMD, but I am not sure
of this. Can anyone shed some

light, please?

-Jose

• Next message: Vibhor Agrawal: "Implementation of ELASTIC NETWORK model in NAMD"
• Previous message: Norman Geist: "AW: questions regarding the source code in NAMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:33 CST