AMBER Archive (2006)

Subject: RE: AMBER: bond information

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Nov 28 2006 - 16:16:03 CST

The mol2 format uses a simpler bond type classification than that of
antechamber. The atom type assignment may be affected (in rare cases) if
only mol2 bond types are considered using "-j 5". Therefore, it is a
better idea to first try "-j 4" to judge bond types. If error occurs,
one may turn to "-j 5" instead.

As a matter of fact, most problem of bondtype is caused by incorrect
connectivity table and a mol2 file can provide a correct connectivity
table. Therefore mol2 file is recommended for the bondtype program.

Hope this will be a help.

Junmei

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Fenghui Fan
Sent: Sunday, November 26, 2006 10:11 PM
To: amber_at_scripps.edu
Subject: AMBER: bond information

Dear all,

As we know, when we use antechamber, sometimes we can
meet the bondtype problem, this is caused by the fact
that the the bond type cannot be judged.

As for the mol2file can give the correct atom type and
bond type, is anyway that we can combine the
antechamber and the mol2 file so that the bond type
judgement problem in antechamber will never occur?

Best regards.

Fenghui Fan

 
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