AMBER Archive (2006)

Subject: AMBER: organic molecule - from newbie :)

From: Raffaella D'Auria (rdauria_at_uci.edu)
Date: Thu Apr 06 2006 - 20:55:02 CDT

Hello,

I would like to simulate an organic molecule (an alcohol) in water. I
have been reading the manual (amber 8) to understand how to build the
force field for a simple alcohol (or to use what is already in the
distribution). However I am not getting very far in understanding how to
do it (meaning how to build the residue and the parameter file).

Should I use antechamber to generate the prep file? And if so how would I
write the pdb file for the alcohol? Is there a list of pdb for simple
organic molecules? I found a pdb file at
(http://xray.bmc.uu.se/hicup/1BO/index.html) but it seems to me that the
atoms types are not in amber format (?), besides there are no H's and I
like to specify the H's too.

Alternatively should I build my molecule using pieces of other organic
molecules that are given in the distribution? If yes how? Is there some
*simple* example I could see?

Thanks a lot!

Raffaella.
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