Thanks.
No, the pdb file you attached has no double-quote characters.
Sorry my mistake. I mixed it up with the CYANA file. I changed the CYANA
files to two back-to-back single quote and it worked fine.
Looks OK to me. Are you still getting exactly this error:?
It works fine now. I might have mixed up the file names.
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.
This is the most important point. I was thinking of removing all the sugar
constraint and in fact you are right about C1'-C1' constraint so I have
deleted them. I think I have to experiment with experimental constraint that
can describe sufficiently the structure of the system.
Raman
On 29 September 2010 15:18, case <case.biomaps.rutgers.edu> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 29 2010 - 14:00:04 PDT
