David,
your patch for link_na.nab is working. Thank you.
Now, I have a problem at the next step.
I want to make some basepairs as you did in program_8.nab for RNA.
I'm using:
setboundsfromdb(b, m, "1:9:", "1:33:", "adna.basepair.db", 1.0);
and I'm getting:
setboundsfromdb: adna.basepair.db, 1:9: -> 1:33: (DT -> DA)
setboundsfromdb: Couldn't find entry for D:P-D:P in adna.basepair.db: 1:9:P 1:33:P
setboundsfromdb: Couldn't find entry for D:P-D:OP1 in adna.basepair.db: 1:9:P 1:33:OP1
setboundsfromdb: Couldn't find entry for D:P-D:OP2 in adna.basepair.db: 1:9:P 1:33:OP2
setboundsfromdb: Couldn't find entry for D:P-D:O5' in adna.basepair.db: 1:9:P 1:33:O5'
.....
--------------------------------------------
On Wed, 6/29/16, David A Case <david.case.rutgers.edu> wrote:
Subject: Re: [AMBER] Library errors while using NAB on Amber16
To: "Slava Chushak" <chushak.yahoo.com>, "AMBER Mailing List" <amber.ambermd.org>
Date: Wednesday, June 29, 2016, 9:53 PM
On Wed, Jun 29, 2016,
Slava Chushak wrote:
> Here
is a nab script:
>
>
molecule m;
> string seq;
> seq = "ATGGCCAATG";
> m = link_na("1", seq,
"", "DNA", "35");
> putpdb( "DNA.pdb", m );
>
> Got an error message
"Residue T not in library nab10.lib."
Wow...I'm guessing no one
has used link_na() in this way for half a decade or
so. The code is using a old,old,old way of
distinguishing between DNA
and RNA, back
from the days when the PDB itself didn't distinguish
between
A and DA (calling both
"ADE").
See the
attached patch file: there are only three lines to be added,
so
you can do this by hand, or do this:
cd $AMBERHOME
patch -p0 < link_na.patch
In either case, type
"make install in the $AMBERHOME/AmberTools/src/nab
directory.
This works for me for you example above. Also
works for RNA (changing T
to U). Let me
know if you find problems. I'll post an update
soon.
Thanks for the
report.
....dac
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Received on Fri Jul 08 2016 - 07:30:03 PDT
