AMBER Archive (2009)

Subject: Re: [AMBER] RDC import from PALES

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Aug 28 2009 - 07:01:30 CDT

On Tue, Aug 18, 2009, Thomas Pochapsky wrote:

[Sorry to be so slow with the reply!]

> We used PALES (a descendant of the Bax SSIA program) to generate
> preliminary alignment tensor components for our experimental NH
> RDCs. We used an AMBER 9-generated PDB file as input for PALES, but
> it required fairly extensive editing,

Can you say what the problems were (hydrogen atom names?)

> Is there a script for generating the RDC .RST file without building
> it by hand?

Yes: see the makeDIP_RST.* files in $AMBERHOME/src/nmr_aux/prepare_input.

> If not, what is the easiest way to determine atom numbers that are
> consistent with our original .top and .crd files for use in the RST
> file?

Use ambpdb to create a pdb file...this will have atom numbers that correpond
to the topology and coordinate files.

...regards...dac

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