VMD-L Mailing List

From: Jacqueline Cawthray (jcawth01_at_gmail.com)
Date: Sun Dec 12 2010 - 18:38:18 CST

I am attempting to use LES (locally enhanced sampling) to look at a
disordered segment in a protein. I am having trouble generating the solvated
and ionized structures of the protein. In the pgn file I included:

multiply 5 A:1 A:16
multiply 5 B:1 B:16
multiply 5 C:1 C:16
multiply 5 D:1 D:16
multiply 5 E:1 E:16

in order to make 5 copies of residues 1-16 in the segments A-E of the
protein. The coordinates in the unsolvated pdb file are in the following:

ATOM 1 CAY ASP A 1 -59.283 -27.111 -32.578 0.00 1.00 A
 C
ATOM 2 CAY ASP A 1 -59.283 -27.111 -32.578 0.00 2.00 A
 C
ATOM 3 CAY ASP A 1 -59.283 -27.111 -32.578 0.00 3.00 A
 C
ATOM 4 CAY ASP A 1 -59.283 -27.111 -32.578 0.00 4.00 A
 C
ATOM 5 CAY ASP A 1 -59.283 -27.111 -32.578 0.00 5.00 A
 C

However when I solvate it is reset to 0 and I cannot ionize (program
crashes).
ATOM 1 CAY ASP A 1 0.000 0.000 0.000 1.00 0.00 A
 C
ATOM 2 CAY ASP A 1 0.000 0.000 0.000 -1.00 0.00 A

ATOM 3 CAY ASP A 1 0.000 0.000 0.000 -1.00 0.00 A

ATOM 4 CAY ASP A 1 0.000 0.000 0.000 -1.00 0.00 A

ATOM 5 CAY ASP A 1 0.000 0.000 0.000 -1.00 0.00 A

Does anyone know if another way to do this? Can the copies be made after
solvating etc and if so, how?

Best regards 

-- 
J Cawthray, Ph.D.
University of British Columbia