On Tue, Apr 28, 2015, Jason Swails wrote:
> >
> > I have an nmr structure that comes from a CYANA calculation and I want to
> > perform a refinement. My pdb file contains 89 residues, but the first two
> > are missing as they are invisible to the technique. Therefore, my cyana pdb
> > file starts up from residue 3 on until res 89.
> > I have successfully changed the atom names according to amber nomenclature.
> > However, when it tries to map atoms using makeDIS_RES it gives some errors
> > as ambpdb generates a pdb file that ranges from residue 1 to residue 87. Is
> > there anyway to tell ambpdb to start up on residue 3? I cannot edit the
> > pdbfile as it is associated with upl and chemical shift files.
> >
>
> I think you can use the "add_pdb" program (or, use the addPDB action in
> ParmEd either from the github repository http://github.com/ParmEd/ParmEd or
> waiting until AmberTools 15 comes out in a week or so -- add_pdb is getting
> replaced by ParmEd in the upcoming release for this task) to add this
> information to the prmtop file (which I think ambpdb will then use to write
> out residue and chain information).
This might trick makeDIST_RST into using the cyana residue numbers. But I'd
recommend (again, in the upcoming AmberTools15 release) looking at the
"cyanarest_to_amberRST" script in
$AMBERHOME/AmberTools/src/nmr_aux/prepare_input. (There is also a
"cyanapdb_to_amberpdb" script there to do the part you have already done.)
Instructions for use are at the top of the script, which converts .upl, .lol,
.aco and .rdc files from cyana to amber format.
I've used these scripts a lot for both proteins and nucleic acids, so I think
they are doing the right thing. But these are fairly new scripts, so problem
reports are most welcome.
...good luck...dac
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Received on Tue Apr 28 2015 - 12:00:03 PDT
