[Xplor-nih] Calculation of palindromic DNA sequencev

[Silke Johannsen, Anorganisch-Chemisches Inst.]

Hello Charles

I tried now to use the dna_refi script but I get always this error:

  X-PLOR>vector do (segid = A) (resid 1:17)
  Assuming literal string "A"
  SELRPN: 525 atoms have been selected out of 1053
  X-PLOR>vector do (segid = B) (resid 18:34)
  SELRPN: 525 atoms have been selected out of 1053
  %VECTOR-ERR: Variable type mismatch between both sides of equation.:
  vector do (segid = B) (resid 18:34)
                                    ^
  %VECTOR-SCPARS-ERR: Assignment aborted.:
  vector do (segid = B) (resid 18:34)

  and after a while the program seems to calculate and stops with this error 
message

InternalDynamics::step: large timestep detected. Halving.

The thing is also that I do not have just the normal bases but also three 
modified ones in a row which coordinate metal ions. Where I have to be 
careful and change things? You also mentioned that I should use a completely 
symmetric potential, but I am beginner and do not know how to do or check 
this. Furthermore I do not have RDCs, do you thing it is possible to get a 
proper structure without them?

thanks a lot

silke


On Tue, 15 Apr 2008 16:59:07 -0400
  Charles at Schwieters.org wrote:

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     Hello Silke--

         I want to calculate a DNA duplex structure with a palindromic 
sequence from NMR data, means I have the NOE restraints only from half of 
the duplex. In my case the center is not a normal Watson-Crick base pair but 
two modified bases, which coordinate linear a metal ion. At first I just 
duplicated the NOE restraints for the others, but the structures looked 
really bad. So the idea was to calculate the upper half, copy it for the 
lower one and set it in the right way together. Is there any possibility to 
do so with xplor NIH? And can I optimize the whole structure afterwards?


     You should really use a completely symmetric potential if when you
     include all atoms- all terms should have the proper symmetry. In
     addition you should use the NCS potential as in the eginput/dna_refi
     example scripts.

     I hope this helps--
     Charles
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