AMBER Archive (2008)

Subject: AMBER: About antechamber and GAFF [UPDATED]

From: Stephane Abel (Stephane.Abel_at_cea.fr)
Date: Wed Nov 26 2008 - 05:21:52 CST

My last message was not very clear,

Below the correct message

Hi AMBER users

I have two little questions about GAFF and Antechamber. Last week I asked a
question about simulations with glycolipid with AMBER force field
(Glycam06 in this case). I received a response of David A Case and Mattew Tessier. They
said me that a good starting point for using AMBER force field and
obtain the partial charge of the molecule is to use Antechamber. So I have installed
Ambertools without any problems and started the tutorials, especially
the example B4 of Ross Walker. If understand well, Antechamber use Gaff
for the assignation of the parameters of the molecule. I try with GAFF, and indeed i obtained the partial charges, for my molecule. Here come my questions, it is
possible to change this force field and use Glycam06 ? Because I want to use only Glycam for my MD If yes, how I can
do it ?

Thank in advance for your help

stefane

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