Hi, Asfa,
NAB (Nucleic Acids Builder) is included in AmberTools1.3
See Professor Case: http://casegroup.rutgers.edu/
A Tutorial by Professor Walker:
http://ambermd.org/tutorials/basic/tutorial1/section2.html
3DNA by Xiang-Jun Lu <
http://www.bussemakerlab.org/lab/> & Wilma K.
Olson<
http://rutchem.rutgers.edu/content_dynamic/faculty/wilma_k_olson.shtml>
See
http://rutchem.rutgers.edu/~xiangjun/3DNA/**
Examples: http://rutchem.rutgers.edu/~xiangjun/3DNA/examples.html
Once you've built your DNA, it is advisable to view it in your favorite
model viewer (VMD and Chimera are free) to ensure you've built exactly what
you want.
If you're using Amber10, the file " all_nuc09.in" contains all the atom
names and types for the various nucleic acids usable by Amber, so checking
it could also be useful.
On Thu, Mar 11, 2010 at 11:40 PM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> If nucgen produces files with outdated nomenclature, what should we use to
> create DNA duplex so that it works well with leaprc.ff99SB (which uses PDB
> Version 3)?
>
> Also I want to create a 22 mer single stranded DNA. What should I use?
>
> Thanks...
> Asfa.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
(631) 913.3194
(561) 635.1848
84hauser.gmail.com
-------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 11 2010 - 21:30:03 PST
