[Xplor-nih] Calculation of palindromic DNA sequencev

[John Kuszewski]

The problem here is that the names you're giving to the segids (A and  
B) need to be in quotes.

If you change your script to read

vector do (segid = "A") (resid 1:17)
vector do (segid = "B") (resid 18:34)

you should be all right.

--JK


On May 30, 2008, at 9:30 AM, Silke Johannsen, Anorganisch-Chemisches  
Inst. wrote:

> 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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