AMBER Archive (2006)

Subject: AMBER: AMBER - leap - problems with impose command

From: Piotr Cieplak (
Date: Fri Dec 15 2006 - 12:18:06 CST

I already tried to post this message but apparently it didn't get through,
or at least I didn't get notification that it went through.
Maybe it was a problem with attachment, so now the message is without

I know that this thread was already addressed by someone on the AMBER list
in the middle of this year, but apparently there was no answer/solution
to that.

I am having problems with understanding why tleap changes orientation of
the coordinates of the molecule in space after changing internal
coordinates by impose command.
When I have a dimer and do impose on one residue belonging to the first
- then this first chain changes orientation in space destroying the whole
The coordinates of the second chain stay intact.
The question is - what is the trick to keep the whole complex intact?

It can be shown by the following tleap command below (and in my setup
in attachment), where I produce three sets of coordinates (pdbs):
a) not modified: coord;
b) after imposing dih angle in one direction along the tree: coord_mod
c) after imposing dih angle along reverse path in the tree: coord_mod_1
Cases b) and c) produces the same results.

cat > <<EOF
source /home/pcieplak/amber10/dat/leap/cmd/leaprc.ff99
aa=loadpdb initial.pdb
saveamberparm aa parmtop.for coord.for
impose aa {38} {
{HG SG CB CA 90.0} }
saveamberparm aa parmtop_mod.for coord_mod.for
impose aa {38} {
{CA CB SG HG 90.0} }
saveamberparm aa parmtop_mod_1.for coord_mod_1.for


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