Thank you very much! I will correct this.
Andrea
-----Original Message-----
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Wednesday, October 20, 2010 7:45 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Residue not recognized
On Tue, Oct 19, 2010, Millen, Andrea wrote:
>
> I created library files for a modified DNA residue using the RED 4
> program and Leap. The nucleoside worked just fine and was recognized
by
> Leap. When I try to incorporate the nucleotide into a DNA strand, it
> fails. When I load my library file in leap, and type 'list' my residue
> (PAA) is present, and when I 'edit PAA' the residue appears as it
> should. When I load the pdb containing the residue, the program does
not
> recognize any of the residues in the strand, even the unmodified ones
Something is badly wrong with the formatting of your pdb file. Atom
names
are supposed to be in 13-16, with one,two and three character names
starting
in column 14, and four-character names (like H2'') starting in column
13.
You have some atom names sneaking over into column 17.
Residue names should be in columns 18-20; two character names (like DA)
are
right justified (columns 19-20) in the PDB, althought I think Amber will
accept left justification as well. Your residue names end in column 21,
so
LEaP thinks the residues are named "D", hence no matches.
Finally, you have some DOS line ending characters in the file. Not
sure, but
this may also cause problems.
It's not clear how you constructed the PDB file, but you need to take
care
that all of the items are in the correct columns.
As a side note: I know it can be very hard to parse the error and
warning
messages from LEaP, but the following things in the leap.log file are a
consequence of the column problem, and therefore something to look out
for:
-- residue 5: duplicate [ H2'] atoms (total 2)
Unknown residue: D number: 0 type: Terminal/beginning
...good luck....dac
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Received on Wed Oct 20 2010 - 10:00:07 PDT
