Thanks for the reply.
Can you cut and paste the *exact* error message? And the line in the cyana
file? I'm not sure if this is some problem comparing a double-quote (")
symbol vs. two single-quotes (''). Also, the spacing and spelling of the
the message above don't make any sense; I'm guessing you typed it in by
hand and made some transcription errors(?)
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
Maybe you (or CYANA) are not making the distinction that amber does between
"
and '' (?) Amber (and the PDB) never use the double-quote character in atom
names.
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?
Are you sure you modified this file correctly? Can you post the modified
file?
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.
The makeDIST_RST file has no notions of "sugars" or anything else, just
atoms
and residues. It is true that the map.DG-AMBER file as distributed is not
set up to take carbon atoms in the sugar ring (is this a pseudoatom for
something else? I'm assuming you don't really have carbon-based NOE's?), so
you will have to add them.
The sugar restraint are not experimental one. They are used by CYANA to keep
the ribose sugar molecule as five-membered.
Raman
On 29 September 2010 10:43, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Sep 29, 2010, Raman Parkesh wrote:
>
> > When I ran the makeDIST_RST to convert CYANA files to AMBER distance
> > restraint, I got this error
> > Error MAP function for H5'' C:data = 1C H5" 1C H6.
>
> Can you cut and paste the *exact* error message? And the line in the cyana
> file? I'm not sure if this is some problem comparing a double-quote (")
> symbol vs. two single-quotes (''). Also, the spacing and spelling of the
> the message above don't make any sense; I'm guessing you typed it in by
> hand and made some transcription errors(?)
>
>
> >
> > Also I changed H5" to H' and ran the makeDIST_RST command again. This
> time
> > the atom was mapped. Is this the right way to edit the file?
>
> Maybe you (or CYANA) are not making the distinction that amber does between
> "
> and '' (?) Amber (and the PDB) never use the double-quote character in
> atom
> names.
>
>
> >
> > Aslo in the CYANA file there were NOE distance restraint for sugar
> molecule.
> > But I am getting the following error
> > Error no MAP function for C4' C:data = 1C C4' 1C 04'
>
> This is correct: there is no C4' atom in the maaping section for residue
> "C"
> in the map.DG-AMBER file. To prevent typos, atoms are not mapped to
> themselves by default--you must include in the file every atom that will be
> involved in a restraint.
>
> >
> > But the error persisted even when the map-DG.AMBER was modified by
> including
> > these atom functions.
>
> Are you sure you modified this file correctly? Can you post the modified
> file?
>
> >
> > The only way I could edit this file was by deleting these sugar
> constraint.
> > I was wondering how we can convert CYANA sugar restraint to the AMBER
> > distance restraint using makeDIST_RES.
>
> The makeDIST_RST file has no notions of "sugars" or anything else, just
> atoms
> and residues. It is true that the map.DG-AMBER file as distributed is not
> set up to take carbon atoms in the sugar ring (is this a pseudoatom for
> something else? I'm assuming you don't really have carbon-based NOE's?),
> so
> you will have to add them.
>
> ....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 29 2010 - 12:00:04 PDT
