AMBER Archive (2003)

Subject: Antechamber atom types

From: Simon Lenzen (simon.lenzen_at_scai.fhg.de)
Date: Tue Mar 25 2003 - 04:41:30 CST

Hello,

we want to prepar a great number of ligands for sander. We have mol2 and
pdb files of this ligands and so we use antechamber.

For some ligands we have checked the assignement of atom types by hand,
based on the description of atom types in "gaff.dat". As already known
there are some problems, but know I have some questions:

1. Does a list off all known errors exist?

2. As mentioned in some mails, they are working on bugfixes for this
problems. Is there any estimation how long this will take?

3. In some cases we are not sure, which atom type is correct. The
explanations in "gaff.dat" are very short. Anybody knows about a more
detailed explanation?

Best regards

Simon Lenzen