VMD-L Mailing List

From: Bernardo Sosa Padilla Araujo (bernardospa_at_gmail.com)
Date: Fri Mar 19 2010 - 23:29:56 CDT

Hi All,

I have two pdb files:

-one of them with an enzyme and its substrate
-the second one only has a very similar substrate( no enzyme)

 I want to load both pdbs, align the substrate from the second pdb to the
substrate in the first pdb, and finally write a pdb file containing the
enzyme (from the first pdb) and the substrate from the second pdb but in
the same position(with respect to the enzyme) as the substrate in the first
pdb.
I have in mind this script :

#molecule 0 is the enzyme +substrate
#molecule 1 is the other substrate
#BAS is the resname of the substrate

# Create a reference structure
set ref [atomselect 0 "resname BAS"]

# Create a selection to align
set sel [atomselect 1 "resname BAS"]
# Move molecule 1 onto molecule 0
set all [atomselect 1 all]
$all move [measure fit $sel $ref]

In order to use writepdb I need to have everything in one selection, but I
don't know how to put structures form different pdb in one vmd slection.
Does anyone know how to do/circunvent this ?
Thanks a lot in advance,

Bernardo