AMBER Archive (2006)

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

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Sun Dec 17 2006 - 01:20:28 CST

No, it does not work that way.
Piotr

On Sat, 16 Dec 2006, Ilyas Yildirim wrote:

> Date: Sat, 16 Dec 2006 06:17:22 -0500 (EST)
> From: Ilyas Yildirim <yildirim_at_pas.rochester.edu>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: AMBER - leap - problems with impose command
>
> 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_at_u-picardie.fr>
>>> Reply-To: amber_at_scripps.edu
>>> To: amber_at_scripps.edu
>>> Subject: Re: AMBER: AMBER - leap - problems with impose command
>>>
>>> Quoting Piotr Cieplak <cieplak_at_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
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
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>
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