Subject: PDB->Sybyl conversion via Babel

From: "Tamas E. Gunda" <[email-masked]>
Date: Fri, 23 Mar 2001 10:19:02 +0100

Dear CCLers:

>I converted PDB structures to the SYBYL format using BABEL.
>The obtained SYBYL structures are not recognized by InsightII (MSI) when I
>try to load it (using the SYBYL format).

 A few days ago there was a similar note on the list.

>While trying to convert a pdb file to mol2 format using babel I get
>the following message without the job being done. The proytein molecule 
>has Mo at its active site .Could anyone suggest how to get around this 
>problem.
>Unable to assign HYB type to atom 1333 type = N
>Unable to assign HYB type to atom 1334 type = N
>Unable to assign HYB type to atom 2344 type = N
>Unable to assign HYB type to atom 3638 type = Mo
>Unable to assign HYB type to atom 7294 type = Mo

On having a closer look on the second problem, the pdb file contained
alternative locations for a few amino acids, this probably interfered with
babel's mechanism for assigning the connections and thus the atom types.
On the other hand, it seems that babel is dealing only with basic atom types
of Sybyl, therefore the molybdeniums were assigned to dummy atoms. (The
extended atom types of Sybyl include all elements). This can be corrected
manually easily. The first problem can also be corrected manually (to remove
one of the alternative atoms), although takes more time to find atoms with the
alternative flag set.

You may use Mol2mol instead of  Babel to convert the files, although the
current version accepts only max 8000 atoms and alternative coordinates may
cause to appear extra bonds.

Best regards

Tamas E. Gunda

-----------------
Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 512 900/2472
fax: (+36-52) 512 914
e-mail: [email-masked]
home-page: www.klte.hu/~gundat/gunda.htm