AMBER Archive (2005)

Subject: AMBER: FW:

From: Andrew Box (box_twin3_at_hotmail.com)
Date: Tue Jul 19 2005 - 21:07:44 CDT

From: "Andrew Box" <box_twin2_at_hotmail.com>
To: box_twin3_at_hotmail.com
Date: Wed, 20 Jul 2005 12:04:23 +1000

Hi

I am trying to add distance constraints to a 6 base pair strand of
DNA with a covalently bound anti-cancer drug. I using a 7 column
restraint file and am trying to make a restraint file for use with
Sander, by using the makeDIST_RST command. I am using the command
as follows:

makeDIST_RST -upb DIST6 -pdb c.pdb -map map.COMPLEX3 -rst RST4

When i run the command i get the following.

[andrew_at_nmrpc3 amber8]$ makeDIST_RST -upb DIST6 -pdb c.pdb -map
map.COMPLEX3 -rst RST4
# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file map.COMPLEX3
ERROR no map function for HC BEN :data= 0 BEN HC 0 BEN H1
            3.07

If delete the first line of the 7 column restraint file, i get a
error with the next line as well.

I created a new map file by copying over the map data for the DNA
base into a new file, then I typed in the data for my anti-cancer
drug (included as attachments are the pdb file of the complex and,
the 7 column restraint file and the map file).

I would appreciate any help you could give me with this.

Thank you

Map file: map.COMPLEX3
PDB file: c.pdb
Restraint file: DIST6

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  • application/octet-stream attachment: DIST6

  • chemical/x-pdb attachment: c.pdb

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