From: Nikolaos Glykos (glykos_at_mbg.duth.gr)
Date: Wed May 25 2011 - 12:15:44 CDT
Hi Massimiliano,
A student of mine tried to prepare a system for NAMD via xleap and
ended-up
with the transformation matrix shown near the bottom of this page :
http://norma.mbg.duth.gr/index.php?id=research:howto:using_the_amber_forcefield
I have not confirmed what she did, and may well all be rubbish (and
this is the
reason I'm not CCing the list).
Nicholas
On Wed, 25 May 2011 16:38:03 +0100, Massimiliano Porrini wrote:
> Dear all,
>
> I am trying to simulate a small protein immersed in a truncated
> octahedron box of water molecules.
>
> Basically I built the box via tleap program of Amber10 and then
> (using
> the vectors component
> taken from Gromacs manual) I passed the box parameters to NAMD config
> files in the
> following way (the "cellOrigin" values were obtained via VMD):
>
>
> 1) MINIMIZATION:
>
> ***
> # Periodic Boundary Conditions
> set dist 58.9627607
>
> set xx [ expr $dist ]
> set xy [ expr $dist * 1/3 ]
> set xz [ expr $dist * -1/3 ]
>
> set yx [ expr 0 ]
> set yy [ expr $dist * sqrt(2) * 2/3 ]
> set yz [ expr $dist * sqrt(2) * 1/3 ]
>
> set zx [ expr 0 ]
> set zy [ expr 0 ]
> set zz [ expr $dist * sqrt(6) * 1/3 ]
>
> cellBasisVector1 $xx $xy $xz
> cellBasisVector2 $yx $yy $yz
> cellBasisVector3 $zx $zy $zz
>
> cellOrigin 29.295766830444336 29.650468826293945
> 29.59993553161621
> ***
>
>
> 2) HEATING:
>
> ***
> # Continuing a job from the restart files
> binCoordinates $inputname.restart.coor
> extendedSystem $inputname.restart.xsc
>
> # Restraints
> constraints on
> consref $filename.pdb
> consKfile $filename.pdb
> consKcol O
>
> # Periodic Images
> wrapNearest on
> wrapWater on
> wrapAll on
> ***
>
>
> Hence at the end of these two processes I should get exactly the same
> box shape and
> dimensions as the one created via tleap (I am using an NVT esemble),
> but
> instead, as you can see from the linked figures, the shape is
> different, since
> the one obtained after NAMD minimization and heating appears to be
> "flatter":
>
> http://www.4shared.com/photo/9kN_g9Qi/amber.html
> http://www.4shared.com/photo/CKpojNEP/namd.html
>
> Do you kindly have any idea/hint about this behaviour?
>
> Should I be worried about a possible rotation of the protein and thus
> a likely interaction with a periodic image of its?
>
> Many thanks in advance.
>
> All the best,
> MP
>
> PS: as one can see from the displayed axes in the two enclosed
> figures,
> the orientation of the system is exactly the same, and the "suspected
> contraction" occurs along the z axis.
>
>
> --
> Dr Massimiliano Porrini
> P. E. Barran Research Group
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini_at_ed.ac.uk
> mozz76_at_gmail.com
> maxp_at_iesl.forth.gr
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
+302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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