Re: AMBER: Question about LEAP and twisting a dihedral angle

From: Ilyas Yildirim <>
Date: Sun, 3 Sep 2006 02:20:27 -0400 (EDT)

Dear Dave,

I have attached the .pdb file I am using. It is a tetramer, (ggcc.pdb).
Here is the I am using:

------------ ------------------
source leaprc.rna.ff99
ggcc = loadpdb ggcc.pdb
impose ggcc { 3 4 } {
  { C3' O3' P O5' 0 }
savepdb ggcc ggcc_new.pdb

The tetramer has 2 strands and I am changing just one dihedral angle of
strand # 1 to zero. The new .pdb file (ggcc_new.pdb) is totally different.
Yes, it keeps this particular dihedral angle at zero degrees; but it
changes all of the atom positions of strand #1 while keeping the atom
positions of strand # 2 untouched. I know that what I am doing is not
right; I need to describe some more restraints to make leap understand
that strand #2 is part of the structure, and that it has to be helical,
but I am not sure how to do it.

Right now, I am writing a script which is going to rotate a structure in a
particular orientation, and plan on doing some complicated procedures
to just change a dihedral angle. Its pretty time consuming and
therefore I am wondering if I can solve this problem with leap, using the
'impose' command. Thanks in advance.


On Sat, 2 Sep 2006, David A. Case wrote:

> On Sat, Sep 02, 2006, Ilyas Yildirim wrote:
> > The impose command does not work; it somehow
> > changes the external coordinates of all of the atoms.
> It would be helpful to post details of the problem. I'm not sure what you
> mean by "external coordinates", but using the impose command is tricky, but
> people in Rob Woods' group have figured a lot out about this. Maybe someone
> could help if you gave details.
> I don't think "twist" works from the command line.
> ...dac
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  Ilyas Yildirim
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Received on Wed Sep 06 2006 - 06:07:02 PDT
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