I tried to increase the force constants because looking for a similar problem into the amber archive i found the following message:
http://archive.ambermd.org/201010/0527.html
The problem was not really the same i got but similar to it.
Thank you for your answer
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: Thursday, April 24, 2014 4:47 PM
To: amber.ambermd.org
Subject: Re: [AMBER] AMBER minimization problem
On Thu, 2014-04-24 at 13:52 +0000, Valentina Romano wrote:
> Hi
>
> I minimized the 6-aminopurine itself twice.
>
> 1) the frcmod (generated by parmchk) was:
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> ca-cc-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
> h5-na-cc-nd 1.1 180.0 2.0 Using default value
> ca-ca-ca-nd 1.1 180.0 2.0 Using default value
> ca-nb-ca-nh 1.1 180.0 2.0 Using default value
> ca-hn-nh-hn 1.1 180.0 2.0 Using default value
> h5-nb-ca-nb 1.1 180.0 2.0 Using default value
> ca-na-ca-nb 1.1 180.0 2.0 Using default value
>
> NONBON
>
> Then, I minimized the ligand in vacuum and without periodicity and the molecule was not planar any more.
>
> 2) I increased the force constants for improper angles and thus the frcmod file was:
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> ca-cc-na-hn 5.6 180.0 2.0 General improper torsional angle (2 general atom types)
> h5-na-cc-nd 5.6 180.0 2.0 Using default value
> ca-ca-ca-nd 5.6 180.0 2.0 Using default value
> ca-nb-ca-nh 5.6 180.0 2.0 Using default value
> ca-hn-nh-hn 5.6 180.0 2.0 Using default value
> h5-nb-ca-nb 5.6 180.0 2.0 Using default value
> ca-na-ca-nb 5.6 180.0 2.0 Using default value
>
> NONBON
>
> Then I ran a minimization as before and the molecule had a planar conformation. So it look like a problem was solved
>
> Then i got an additional problem:
> I created topology and coordinate files for the 6-aminopurine-PknG complex (following the steps of the tutorial B4) and of course i used the ligand's frcmod file manually modified (which worked for the ligand alone).
> Then i minimized the complex:
>
> Initial minimisation of PknG-Adenine complex
> &cntrl
> imin=1,
> maxcyc=500,
> ncyc=250,
> ntb=0,
> igb=0,
> cut=12
> /
>
> After the minimization the 6aminopurine within the binding pocket had
> lost again is planarity. It had a distorted conformation.
>
> Do you have any idea of how i could avoid the ligand distortion when i
> minimized the whole complex and not only the ligand itself?
So you increased the force constant from 1.1 to 5.6 for all of the
improper torsions (which are the parameters typically used to maintain
planarity). This kept the isolated ligand planar during a minimization.
This means that there were _some_ forces (probably non-bonded forces)
that were pushing the molecule away from planarity harder than the
impropers were trying to keep the molecule planar. When you made the
impropers stiffer, they were able to overpower the effects that were
resisting planarity.
When you embed it in the system, it loses its planarity again. This
indicates that there are now even _stronger_ forces pushing against
planarity than there were outside of the bound complex that can now
overcome the strength of the 'stronger' improper terms. It stands to
reason that making the force constant even stronger will keep the rings
planar more.
Force fields are remarkably simple -- there is a simple functional form
for the interaction of particles from which the reasoning I used above
naturally follows.
However, adjusting the force field to get the results you expected to
get in the first place is bad science in my opinion. Force fields are
parametrized against experimental measurements or higher-level quantum
mechanical calculation. Unless you can justify your changes to the
parameters with something besides "I think this molecule should be
planar" there is no reason to trust your new parameter set. (And as
Dave mentioned before, assuming that your 6-amino purine is planar in a
bound complex is not necessarily accurate -- it could very well be
non-planar when bound in a complex).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 24 2014 - 08:30:03 PDT
