Subject: Sybyl_mol2 files for DOCK4.0

From: [email-masked]
Date: Thu, 27 Jun 2002 17:45:09 +0200 (CETDST)

Hello everybody,
I've got a lot of questions for you!
I'm a new Dock4.0 user, unfortunately I do not have access to the Sybyl suite of
programs so I have to obtain mol2 files for docking in alternative ways.
I've tried writing Sybyl_mol2 files with InsightII both for proteins (pdb files)
and for ligands database (mdl files obtained by Catalyst and then convert in sd
files by Babel). For the protein (I've selected Amber98 ff) the sybyl atom types
were not correctly assigned (no N.4 atom type was assigned to the positively
charged aminoacid according with the Tripos force field, carboxylic oxigen were
labelled as O.2 instead of O.co2 and so on...)
For the ligands databases in .sd format (cvff force field selected),often
InsightII does not recognizes correctly the bond orders and consequently does
not assigns proper charges and atom types. The automatic modification of bond
orders within InsightII seems to me not to work well on all molecules. I have
also encountered problems in assigning partial charges with cvff to positively
charged molecules such as protonated triazine derivatives.

My questions are:
Do someone have similar problems?
Is there an alternative procedure to obtain mol2 files appropriate for dock4.0?
(mol2 files obtained by Babel lacks the SUBSTRUCTURE section which is required
by dock4.0)
Is there a way (a freeware script or something like that) to assign partial
charges to a mol2 file obtained by the sdf2mol2 utility of dock?
Have someone ever used the "chunks" executable of Dock to add Gasteiger-Marsili
to mol2 files?  

Any suggestion would be appreciated,
thank you in advance.

Sara

Pacchioni Sara
Ph D Student
Department of Medicinal Chemistry
University of Modena And Reggio Emilia
Via Campi 183
41100 Modena
Italy
+39-059-2055122
e-mail: [email-masked]