Hi Michael,
I don't know whether this solves your problem, but you can play around
with the vanderwaals parameters:
In your script (asuming xplor syntax. I don;t know how this looks in
pyxplor syntax) you can use the parameter nbonds statement:
parameter
nbonds !p33 and further in manual
repel=0.70 ! multiplication of vdw radius
rexp=2 ! Exponent for repel-function (p.76 manual)
irexp=2 ! irexp for repel function
rcon=1. ! Energy constant for repel function
nbxmod=4 ! Unleash potential p.37 manual
wmin=0.01 ! Threshold for close distance warning
cutnb=4.5 ! nonbonded interaction cutoff radius
ctonnb=3.49 ! Radius at which the switching function becomes
effective
ctofnb=3.50 {Modified, MvD} !! Radius at which the switching
function sets nonbond energy to zero
tolerance=0.5 ! Distance an atom can move before updating
nonbonded energy
!inhibit=0.25 !Distance at which vdw energy is truncated
end
end
The number after is the factor by which the vanderwaals radius of an
atom is multiplied in order to calculate its vanderwaals energy.
The manual I refer to is the book:
Brunger, A.T. (1992): X-PLOR, Version 3.1 A system for X-ray
Crystallography and NMR, Yale University Press, New Haven, ISBN
0-300-05402-5
An updated version can be found at:
http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/
(A PDF version also exists, but the pagenumbering does not match with my
comments. I could not find the PDF version now, if you want to I could
mail you a cooy of the PDF I have here on this computer)
Regards,
Ramon van der Werf
Radboud University Nijmegen
The Netherlands
On Sun, 2007-03-18 at 14:13 -0400, xplor-nih-request at nmr.cit.nih.gov
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> Today's Topics:
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> 1. request for some help (Michael Hodsdon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 18 Mar 2007 10:12:50 -0700 (PDT)
> From: Michael Hodsdon <mehodsdon at yahoo.com>
> Subject: [Xplor-nih] request for some help
> To: xplor-nih at nmr.cit.nih.gov
> Message-ID: <547815.79033.qm at web82114.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> ***
>
> I have made multiple attempts to send this message to the list and I am not
> sure what I am doing wrong. So, if it ends up that I have sent a number of
> copies of the same message to everyone's inbox, I sincerely
> apologize.
>
> ***
>
>
> Greetings All,
>
>
>
> I have previous experience using CYANA to calculate structures using NOE
> restraints. Now, I am trying to include RDCs and am migrating over to
> Xplor-NIH. I am having a few difficulties and was hoping to "beg" for
> some assistance/advice.
>
>
>
> We are working on a 150 residue protein. We have nearly complete (97%)
> assignments and have picked a large number of NOESY correlations from 3D
> NOESY-HSQC spectra. Using "NOEASSIGN" (previously known as CANDID) in
> CYANA, these NOEs were easily assigned in a fully automated manner
> resulting in a nicely converged ensemble of structures (backbone RMSD <
> 1 Angstrom).
>
>
>
> We next converted the ~3000 independent distance restraints from CYANA
> to Xplor-NIH format. This was no easy task given the very different ways
> that CYANA and Xplor-NIH handle non-stereospecifically assigned
> hydrogens. I am fairly certain that the conversion utility bundled in
> CYANA 2.1 does NOT convert the NOEs correctly. I ended up writing my own
> AWK script to do it. Has anyone else tried to do this? I am fairly
> confident that my conversion is correct as I was able to import the
> converted restraints into Xplor-NIH and test them against one of the
> fitted structures from CYANA (which also had to be converted!) and got
> agreement.
>
>
>
> Surprisingly, when I try to use Xplor-NIH to calculate ensembles of
> structures using these converted distance restraints, I CANNOT achieve
> as good convergence as I could in CYANA. Using a local Beowulf cluster I
> calculate 100 structures and keep the best 20-40. I always had 10 - 20
> frequently violated NOEs and a LOT of VDWs violations (20 - 60). I am
> guessing this is a consequence of the difference in the potential
> (pseudo-energy) functions used for the two methods. For example, in
> Xplor-NIH I am using this "RAMA" term, which I don't think there is an
> equivalent in CYANA.
>
>
>
> I began to suspect that my distance restraints from CYANA were just a
> little to "tight" (and thus conflicting with other terms in the
> potential function). So, I went back and loosened them up a bit (with
> CYANA's calibration routine) and I got many fewer NOE violations, but
> still a lot of VDW violations. Still, I felt this was progress.
>
>
>
> At this point, I had finally measured RDCs in Pf1. I started by just
> throwing in the N-N RDCs along with the above described "looser" NOEs. I
> used one of the example refine.py scripts (attached) and I took one of
> the fitted structures from CYANA as the starting model. The calculated
> structures are in good agreement with the RDCs (which was very nice to
> see) with tensor values of approx -16 and 0.6 (Da and Rh). But, I still
> get more NOE and VDW violations than I was expecting.
>
>
>
> I have to keep the identity of this protein a little quiet, but I have
> attached the refine.py script and the ".xplorInput_##.sa.stats" output
> file. Overall, the structures look the same as those created by CYANA,
> but they aren't as precise and the geometry isn't as good. There must be
> something I am doing wrong and I would love for some to point it out for
> me.
>
>
>
> Many, many thanks to anyone who read this far.
>
>
>
> Mike
>
>
>
>
>
>
>
>
>
