AMBER Archive (2006)

Subject: AMBER: Antechamber & atom types

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Apr 20 2006 - 12:04:17 CDT

Dear All,

I use antechamber to generate FF atom types for Tripos mol2 files coming from
R.E.D. (multi-molecule & conformation & orientation RESP fit for more than 100
structures):

foreach mol2 ...
  antechamber -i Mol-from-R.E.D.-III.mol2 -fi mol2
              -o Mol-GAFF-atom-types.mol2 -fo mol2
end

I used two versions of antechamber: the version 1.25 from the antechamber web
site and the version from amber8 (patches 3 6 and 8 applied). All the atom
types were well assigned for all the structures. However, the two versions of
antechamber do not find the same atom types for one type of hydrogen (h4 or ha)
for one class of molecule:

 R ha|h4 (h4 is found by the version 1.25)
  C = C
 R Cl

Which one is the right one ?

Thanks, regards, Francois

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