On Wed, Jan 06, 2010, Donald Thomas wrote:
>
> I'm trying to run through the basic tutorial for building DNA. I have built
> Amber 10 on two Ubuntu 9.10 boxes and applied all bugfixes. The
> installations were both successful and the tests only result in a handful of
> failures that were not significant.
>
> Whether I build the pdb file myself or use the one supplied in the tutorial
> I end up with half the DNA not being recognized (even after addition of TER
> cards). In xleap it shows up as the attached picture.
>
> It tried AmberTools 1.3 with the same result.
>
> However, if I change to a forcefield other than ff99* such as ff02pol.r1 or
> ff03 the file loads perfectly.
>
This is a known problem, but I haven't had any luck in getting someone to
update the tutorial:
http://dev-archive.ambermd.org/200907/0004.html
The problem is that the "nuc.pdb" file in the tutorial uses an outmoded
nomenclature: you need to change "T" to "DT" in the second strand: there is
no RNA version of thymine!
The following NAB program could be used in place of nucgen:
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");
See: http://dev-archive.ambermd.org/200907/0007.html
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 05 2010 - 21:00:05 PST
