Dear CCL Subscribers,
I am presently using amber, (for the first time) to model tetrolic acid. I
have a number of queries relating to my attempt
1: What is the most appropriate atom type for the sp2 carbon single bonded
to one oxygen and one carbon and double bonded to an oxygen. I have chosen
the C atom type.
2: What is the most appropriate atom type for the sp carbon single bonded to
one carbon and triple bonded to another carbon. I have chosen CM.
3: What is the most appropriate choice for the oxygen in the carboxyilic
acid that is double bonded to a carbon atom. I have chosen 02.
4: What are the most appropriate angle parameters for the 0H-C-O2 and
OH-C-CM bond angles and what literature can they be sourced in.
The OS I will be using is linux 2.4
I am not sure which version of Amber I will be using but I will use a force
field file contributed to the gormacs site with details as given at this
address:
http://www.gromacs.org/contributed_by_users/task,doc_details/gid,13/
Thank you in advance for your assistance.
Russell Glavey
russellglavey.hotmail.com
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Received on Sun Dec 24 2006 - 06:07:23 PST
