On Mon, Nov 30, 2009, Wallace Kunin wrote:
> I used tleap and left out the quotation marks. Here is the output:
>
> > model = loadpdb nuc_ter.pdb
> > Loading PDB file: ./nuc_ter.pdb
> > Unknown residue: A5 number: 0 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: A3 number: 9 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: T5 number: 10 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: T number: 11 type: Nonterminal
OK, I see know. You should probably use
http://w3dna.rutgers.edu (or
the fd_helix routine in NAB, see below) to construct your structure.
The ancient, ancient "nucgen" program is putting out very old-fashioned
residue and atom names (e.g. "T" instead of "DT", etc.).
Volunteers needed! Can someone fix up tutorial 1 to get some starting
structures that have modern nomenclature? ...thanks...
[I *think* all one has to do is the following:
1. create the following nab file, fd.nab:
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");
2. compile and run it:
nab fd.nab
./a.out
This looks to me like it will get users going.
...dac
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Received on Mon Nov 30 2009 - 12:00:02 PST
