Thank for this. CYANA files did work pretty well in the AMBER. However I
have some question on the program makeDIST_RST.
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.
I checked the CYANA restraint file, pdb file and the map-DG.AMBER file and
this atom was MAPPED in the residue C of map-DG.AMBER. Why I am still
getting the error. Does map-DG.AMBER has some database which it checks and
if the atom is not defined it will give error? or Do we have to define a
complete new residue in map-DG.AMBER?
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?
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'
But the error persisted even when the map-DG.AMBER was modified by including
these atom functions.
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. Do you have the define new Residues
for sugar in the map-DG.AMBER or we can manually include the sugar restraint
in the .RST file already generated without sugar restraint.
I was checking the makeDIST_RST -help and the AMBER manual but there is not
that much information about this.
Any suggestion or comment will be useful.
Thanks
Raman
On 29 September 2010 08:01, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Sep 24, 2010, Raman Parkesh wrote:
>
> > I wanted to convert Xplor generated NOE restraint (tbl) to AMBER
> restraint
> > file. I was wondering if anyone know or has script for this. Any help
> will
> > be appreciated.
>
> You might check out the AQUA program, http://nmr.cmbi.ru.nl/~jd/aqua/; the
> web page may be outdated, so contacting the author, Jrugen Doreleijers,
> might
> also help. Amber can use DIANA formats, so conversion from xplor to DIANA
> might be a first step.
>
> I've not used these programs myself, so this advice might be off-base. But
> if
> anyone knows the answer, I would think it would be Jurgen.
>
> ....dac
>
>
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Received on Wed Sep 29 2010 - 06:30:05 PDT
