From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Fri Nov 05 2010 - 16:21:05 CDT

My question is real basic, but produce many problems so far, so any
sugestion is strongly welcomed. I need to calculate rgyr for NAMD2.7b2
trajectory (10000 frames) for atoms having serial numbers 7 8 9 10 11 12
13 14 15 19. PDB, PSF and DCD ar not for the protein, so only way to
make correct selection is likely

"mol modselect 0 0 serial 7 8 9 10 11 12 13 14 15 19"

when try to define this selection as

  set disat [mol modselect 0 0 serial 7 8 9 10 11 12 13 14 15 19]

, likely that selection could not be recognized - empty command name ""
- for simple function, for example $disat num .
Next when I try to calculate rgyr by using

measure rgyr atomselect "mol modselect 0 0 serial 7 8 9 10 11 12 13 14
15 19" [weight mass]

(or same without atomselect or with differently positioned first
quaternion mark) I can not obtain results. Second problem is definition
of weight, which should be [weight mass] - lways receive message that
"weight" is invalid command name
I using VMD 1.8.7 Win version

Thank you very much in advance

Branko

P.S.

First two lines of the PDB atom record looks like this for orientation

ATOM 1 C1 UNK A 1 -2.265 2.415 1.070 1.00 0.00
A1 C
ATOM 2 C2 UNK A 1 -2.345 3.239 -0.042 1.00 0.00
A1 C