VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 28 2010 - 16:52:12 CST

Hi,

First, your commands as written only multiply residues 1 *and* 16. You
need to list every residue to get them all (and if they are bonded they
need to all be on the same line):

   multiply 5 A:1 A:2 A:3 A:4 A:5 A:6 A:7 A:8 A:9 A:10 \
              A:11 A:12 A:13 A:14 A:15 A:16

I'm not sure why the coordinate is being reset to zero, but I can say that
the coordpdb command will not work with a LES pdb file because it is based
on atom names, not their sequence in the file.

You need to do the LES multiply step last. Solvate the system, minimize,
and possibly even equilibrate the system as usual, then reload the psf and
pdb files, run the multiply commands, and write out.

-Jim

On Sun, 12 Dec 2010, Jacqueline Cawthray wrote:

> 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
>