On Tue, Apr 28, 2015 at 1:32 PM, Miguel Ángel Mompeán García <
mig.mompean.gmail.com> wrote:
> Dear all,
>
> 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).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 28 2015 - 11:00:03 PDT
