ADL: how to prepare ligands in pdb format

Michael Popov popov at enzyme.siobc.ras.ru
Wed Feb 9 05:50:45 PST 2005


Dear yuchen,

As far as I know there are some specialized commercial tools (Corina),
but the commonly used and free for academic society is PRODRG server,
the engine of it is now available for download (below is the quotation
from the developer).

> Dear all
>
>  The PRODRG2 program, which generates coordinates and topologies from
>  scratch (output formats: various PDB files with/without hydrogens and CNS,
>  REFMAC, SHELX, WHAT IF, O, MDL Molfile, Mol2, Gromacs, Autodock (and
>  others) topologies) is now available as a binary executable for free for
>  academic users.  Please download and use PRODRG locally if you want to,
>  for instance, convert large libraries of small molecules - this will
>  relieve some of the strain on the server, which is still there for anyone
>  to use and always runs the most up-to-date/bug-fixed version.
>
>  In addition, a new version, PRODRG2.5, is available for testing on the
>  server (and will also soon be available for downloading). There are
>  several improvements, the most significant improvement is compatibility
>  with the Gromos96 force field. PRODRG2.5 is very much a beta version and
>  we would welcome your feedback to help us improve it.
>
>  The server/download page is at http://davapc1.bioch.dundee.ac.uk/prodrg
>
>  Happy PRODRG-ing and best wishes for 2005!
>
>  Alex Schuettelkopf & Daan van Aalten
>
>  ##############################################################################
>  Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
>  Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
>  Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
>  School of Life Sciences                E-mail: see WWW page
>  Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
>
> ________________________________________________


Wednesday, February 9, 2005, 9:58:32 AM, you wrote:

ybso> dear all,

ybso> i have quite a number of ligands in .pdb format. seems it is very
ybso> unrealistic for me to manually prepare them using ADT. anyone has idea how
ybso> to automate this preparation process? by writing python scripts?

ybso> thanks a lot!

ybso> best regards,

ybso> yuchen
ybso> ________________________________________________
ybso> --- ADL: AutoDock List  ---
ybso> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---


-- 
Best regards,
 Michael                            mailto:popov at enzyme.siobc.ras.ru




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