From: mvitod (
Date: Tue Jan 22 2013 - 12:52:30 CST

Dear all,
We are trying to pull the ligand out of the enzyme active site using
the SMD. First we tried the method described in “NAMD Tutorial” (example
with ubiquitine) and that worked just fine. But as we wanted to
simultaneously extract the distance between the SMD and fixed atom (and
in order to avoid huge .dcd files), we have used the smd.tcl script from
“Stretching deca-alanine” tutorial. The SMD atom was centroid defined
from positions of three C atoms on phenyl ligand group. But we have few
problems with that. The pulling direction is wrong, and in the smd.out
file we got negative values for the distance. We tried to use the actual
coordinates of the SMD atom and fixed atom (as described in tutorial),
or even normalized vector values, and also the differences of the
coordinates (X2-X1, Y2-Y1, Z2-Z1). I cannot figure out what is wrong
with our entries in the smd.tcl script.
Respective parts of our smd.tcl script are:

# Atoms selected for force application

set id1 3079 #fixed atom
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1]

set id2 8423 #numbers of the three C atoms used to define the centroid
on the ligand
set id3 8425
set id4 8427
set grp2 {}
lappend grp2 $id2
lappend grp2 $id3
lappend grp2 $id4
set a2 [addgroup $grp2]

# constraint points
set c1x 0.0
set c1y 0.0
set c1z 0.0

set c2x 10.362
set c2y 12.839
set c2z -8.639 –these are coordinate differences X2-X1, Y2-Y1, Z2-Z1

Thanks in advance,
Maja Vitorovic

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