On Sat, May 07, 2011, Sindrila Dutta banik wrote:
>
> As I run the dna1=loadpdb it shows some error message as follows-
>
You input pdb file ("prepared by glactone") has some serious problems.
First, the atom names are in the wrong columns; second, it has very
non-standard atom names (like HTER, OXT, etc.); third, the residue names
are for RNA, not DNA. Basically, you need to follow the rule: "keep
fixing the pdb file until leap stops complaining."
> -- residue 1: duplicate [ H2'] atoms (total 2)
These errors arise because the atom names are in the wrong columns.
> Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5.
Note that "G" means a ribo-nucleotide, not a deoxyribonucleotide. You need to
use "DG" if you want a deoxy nucleotide.
> (Residue 6: T, Nonterminal, was not found in name map.)
Same problem: there is no "T" residue.
Unfortunately, amber has no simple procedure to prepare initial Z-DNA
fragments with arbitrary sequence. You might try
http://w3dna.rutgers.edu,
although that site seems to be down right now. Otherwise, hand-editing the
file you have may be required.
....dac
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Received on Sat May 07 2011 - 07:00:02 PDT
