Hi Asfa,
> If nucgen produces files with outdated nomenclature, what should we use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)?
>From section 2.1.1
So, with this in mind we can construct the input file required by NAB to
build our 10-mer polyA-polyT DNA duplex in the Arnott B-DNA canonical
structure. This program is given below. Basically, this is building two
strands of A-T paired DNA. For more specific information about the various
options, see the manual.)
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");
Put the above into a plain-text file called nuc.nab.
...
of
http://ambermd.org/tutorials/basic/tutorial1/section2.htm
> Also I want to create a 22 mer single stranded DNA. What should I use?
You should also be able to do this with NAB. Or indeed just take the pdb
from above and delete the second chain.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Thu Mar 11 2010 - 21:00:07 PST
