Re: [AMBER] Problem in preparation of log file

From: case <>
Date: Sat, 7 May 2011 09:37:25 -0400

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,
although that site seems to be down right now. Otherwise, hand-editing the
file you have may be required.


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Received on Sat May 07 2011 - 07:00:02 PDT
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