On Wed, Sep 29, 2010, Raman Parkesh wrote:
>
>
> I have pasted the "exact' error messages here and also the cyana input line.
>
> ERROR no map function for H5" C :data= 1 C H5" 1 C H6 3.75 5.00
> # error from the makeDST_RST command line
>
> 1 C H5" 1 C H6 3.75 5.00
> # line from cyan
OK: just as I indicated before, cyana is using a double-quote character(")
where Amber and the pdb use two back-to-back single quotes ('') You will need
to fix the cyana file.
>
> I have attached the CYANA input file and the the energy minimized pdb file
> which I generated using ambpdb program. The pdb file contains double-quote
> character?
No, the pdb file you attached has no double-quote characters.
> I have attached the modified map-DG.AMBER file. I am not sure if the mapping
> I did is in correct format. I did mapping in the residue C.
Looks OK to me. Are you still getting exactly this error:?
> > > Error no MAP function for C4' C:data = 1C C4' 1C 04'
(aside from the typos in the hand-transcription)?
Of course, in Amber, there is no need to have a restraint between C4' and O4'
anyway...In fact, all of the cyana "sugar" constraints (involving carbons)
seem to be devoted to getting sugar pucker or something correct, and there
are things like C1'--C1' restraints at 10 Ang. that seem to assume a
near-perfect double helix, etc. Even after you solve the file format
conversion problem, you will need to think about the scientific content and
origin of the constraints, and decide which ones you need to keep.
....dac
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Received on Wed Sep 29 2010 - 12:30:06 PDT
