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
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Received on Wed Sep 29 2010 - 08:00:04 PDT
