Any coordinates in the PDB files that you load will override the coordinates
of the Amber prep file that you can download from the Bryce website you
gave. I agree there is one bond that looks slightly odd, but this will not
affect the coordinates in your PDB file if that atom is already there.
Make sure that your atom names in the PDB file (and residue name) match the
names found in the Amber prep file that you downloaded from that website,
otherwise you will get weird added atoms.
The parameter files on that site are fine, and I suggest using them.
Good luck!
Jason
On Fri, Dec 31, 2010 at 10:36 AM, Jacopo Sgrignani <sgrigna.sissa.it> wrote:
> Dear Amber users
>
> i'm looking for Guanosine triphosphate parameters , i found some files
> on the web page of the Manchester Univ.
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> But if I save a simple pdb form these libraries i got a wrong
> structure, whit a strange oxygen.
>
> Could anybody help me to find a correct parameter file?
>
> Thanks and happy 2011!
>
> Jacopo
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by Horde http://www.horde.org/
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 31 2010 - 16:30:02 PST
