AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Sun Sep 03 2006 - 10:55:16 CDT

On Sun, Sep 03, 2006, Ilyas Yildirim wrote:
>
> 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.

NAB has a nice interface here, at least for some problems. It lets you
specify which atoms are to move, as well has making it easy to construct and
apply a rotation about an arbitrary axis. The (known) problem with "impose"
is that it has to try to guess which atoms to move.

I'm cc-ing this to Wei Zhang, so that maybe gleap will be smarter.

..thx...dave

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