My solution with impose is this:
1. Load the .pdb file in Leap and save it as temp.pdb.
2. Remove the second strand strand from temp.pdb (which does not have any
dihedral change), and save the rest of the file as temp1.pdb.
3. Save the removed part of the temp.pdb (namely the second strand) as
temp2.pdb.
4. Load the temp1.pdb in Leap, and use the 'impose' command to change the
dihedral angles. Save the file as temp3.pdb
5. Combine temp2.pdb with temp3.pdb; call it temp_final.pdb.
Hope this helps. Best,
On Fri, 15 Dec 2006, Piotr Cieplak wrote:
> Also - there is another problem. If I have a monomer only - and try to
> change a diedral angle - then the whole molecule moves out of its initial
> position in space. It never happens in old EDIT program. And sometimes it
> is important for some application.
> P.
>
>
> On Sat, 16 Dec 2006, FyD wrote:
>
> > Date: Sat, 16 Dec 2006 07:22:36 +0100
> > From: FyD <fyd.u-picardie.fr>
> > Reply-To: amber.scripps.edu
> > To: amber.scripps.edu
> > Subject: Re: AMBER: AMBER - leap - problems with impose command
> >
> > Quoting Piotr Cieplak <cieplak.cgl.ucsf.edu>:
> >
> >> 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
> >> chain
> >> - then this first chain changes orientation in space destroying the
> >> whole complex,
> >> The coordinates of the second chain stay intact.
> >> The question is - what is the trick to keep the whole complex intact?
> >
> > I wonder if it is not a normal feature, I mean in LEaP. I might be wrong but
> > I wonder if the same thing also appends with 2 DNA strands... It appends also
> > in InsightII (Accelrys Inc). My understanding of this is that each time you
> > move an atom a part remains fix and another moves. I guess if you have no
> > chemical bond between your two chains, it is normal the second one does not
> > move if you change the 1st one. I think if your 2 chains were bounded it
> > would be different. What about trying this sequence ?
> >
> > - load your structure in LEaP
> > - Create a temporary bond between your 2 chains/change the molecule topology
> > - do your impose command
> > - remove the temporary bond created/rebuild the initial topology
> >
> > regards, Francois
> >
> >
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>
--
Ilyas Yildirim
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- University of Rochester - -
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Received on Sun Dec 17 2006 - 06:07:28 PST
