Dear Jason
Thank you for your answer.
As you said, even increasing the force constants the molecule was still slightly flexible.
I will try to increase more the force constants and see what appends.
By the way, I already tried to apply the NMR restraints( explained in chapter 23) and I thought that the "natural language" was a good way to apply them.
I thought i did understand how to use this system to define restraints, since applying it none restraints are applying on my complex.
The minimization file together with the restraints part is the following:
Initial minimisation of PknG-Adenine complex
&cntrl
imin=1, maxcyc=500, ncyc=250,
cut=12, ntb=0, igb=0,
&end
&rst
iat=1,
restraint = "angle(plane(3838,3841,3841,3843),plane(3837,3836,3836,3834))
r1=-180, r2=0.0, r3=0.0, r4=180,
rk2=100, rk3=100,
&end
The first plane is the benzene ring and the second the imidazole ring.
Is it wrong?
All the best
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Wednesday, April 30, 2014 1:51 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Minimization with restraints
On Wed, 2014-04-30 at 09:42 +0000, Valentina Romano wrote:
> Dear Amber users
>
> I want to run a minimization of a protein binds to an aromatic planar molecule (2 aromatic rings fused).
>
> I would like to keep the molecule planar during the minimization applying restraints on it, but i have not experience in it.
> Do you have any suggestions?
After having a conversation with one of my colleagues, it turns out that
purine planarity is a known problem in nucleic acid simulations. If you
make the improper torsions you were modifying even stronger (by
increasing the force constant), does it solve your planarity problem?
It should still be slightly flexible (so don't make the force constant
*too* stiff), but apparently not as flexible as you are seeing.
Personally I think if you are going to force planarity with a restraint,
you might as well use an improper torsion to do it instead. That said,
you can use the NMR restraints (chapter 23 of the Amber 14 manual, and
see the test case in $AMBERHOME/test/nmropt/pme/nmropt_1_torsion for an
example).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 30 2014 - 06:00:04 PDT
