Hi Donald,
The format for DNA pdb's has recently changed and AMBER has been updated to
support this. However, nucgen produces an old style pdb that is no longer
recognized. As such the tutorial requires updating. I am in the process of
doing this and will post an updated version shortly.
Sorry for the inconvenience. For the moment you can either proceed using the
prmtop and inpcrd files supplied or as you found us FF03 which has not been
patched with the new DNA residue naming conventions.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Donald Thomas
> Sent: Tuesday, January 05, 2010 8:31 PM
> To: amber.ambermd.org
> Subject: [AMBER] ff99SB in DNA tutorial
>
> Hi,
>
> 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.
>
> Any ideas.
>
> Don Thomas
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Received on Tue Jan 05 2010 - 21:00:04 PST
