RE: [AMBER] Difference of ff99 and ff03 in building DNA duplex

From: Ross Walker <>
Date: Thu, 11 Mar 2010 20:49:40 -0800

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 If nucgen produces files with outdated nomenclature, what should we use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
> 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



> 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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Thu Mar 11 2010 - 21:00:07 PST
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