Subject: Problem in reading PDB files

From: Arthur Wang <[email-masked]>
Date: Fri, 8 Dec 1995 20:38:19 -0800 (PST)

Dear CCLers,

Have you ever used SYBYL? During the last few days, I was astonished to 
find SYBYL does have problem in reading PDB files. Let me elaborate now.

First, I constructed several organic molecules by QUANTA 4.1 then I
exported them in PDB files. But when I wanted to perform further QSAR
studies on these molecules in SYBYL, I found SYBYL could not read them
properly. Oftenly aromatic carbons were ignored and atom connections could
not be rebuilt. I checked my PDB files carefully, but I just got no idea. 
Feeling frustrated, I attempted to use SYBYL to construct a model for
test. I saved it in several PDB formats, such as Brookheaven, AMBER
Brookhaven and DSCG Brookheaven, which were all listed in the SYBYL menu. 
When I tried to recall my model from these PDB files, I failed again. It 
seems that SYBYL does not recognize its own output!

You can check it yourself by constructing a molecule as simple as 
biphenly. When you recall it from the PDB file, I am sure you will find 
several aromatic carbons are missing.

Anyone who has noticed this problem? Or you have good ideas to deal with 
it? Or you have found my mistake?

Arthur in desperation.

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_/                                                        _/ 
_/   Arthur Wang                     Doctoral Candidate   _/
_/                                                        _/           
_/   Molecular Design Lab                                 _/
_/   Institute of Physical Chemistry, Peking University   _/
_/   Beijing 100871, P.R.China                            _/
_/                                                        _/ 
_/   E-mail: [email-masked]                        _/
_/   Tel: 86-10-2501490    Fax: 86-10-2501725             _/
_/   WWW: http://www.ipc.pku.edu.cn/arthur/homepage.html  _/
_/                                                        _/ 
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From: David Larson <[email-masked]>
Date: Fri, 8 Dec 1995 11:30:49 -0600 (CST)

Dear Dr. Wang

I built biphenyl as you described and found that the problem you were 
having is due to the substructure name PHENYL is truncated to PHE when 
writing out to a PDB file. When reading the file back in, Sybyl is 
interpreting the PHE substructure as phenylalanine, rather than phenyl. 
Modifying the substructure name will solve your problem.

Please keep in mind that the PDB file format supports connectivity for 
amino acids and is not the best file format for saving small organics.
As such, importing small organics from PBD format into Sybyl will result 
in aromatic carbons being modeled as sp2 carbons.

Better file formats to use for organics are Sybyl MOL2, MACCS SD, and MACCS MOL.

A quick way to change C.2 atoms to C.ar in Sybyl is to modify the atom types 
using the following SPL:

   for i in %sln_search2d(m2 C=C=C nodup normal 2)
   modify atom only $i c.ar
   endfor

Note that you might want to use C=C(Any)=C as the query except that this
won't pick up C=C(=Any)=C which may connect phenyls.

Please let me know if you have any questions.

Best regards,
David

David Larson				e-mail:	  [email-masked]
Customer Support Scientist		phone:    314-647-1099
TRIPOS Inc.				fax:      314-647-9241