AMBER Archive (2004)

Subject: AMBER: cys protecting group parameters

Date: Fri Jul 09 2004 - 08:48:36 CDT

Dear all,

I'm performing MD simulations on peptides containing Cys residues as they are. I would like to perform simulations even with the cys protected with an acetamidomethyl group, but there are some missing parameters in the parm99 for this group, expecially regarding the angle bendin terms involving the sulphur atom. Are there any available parameters for this group (or other protecting groups) and what is the best choice fot the sulfur atom tipe? Antechamber suggests S, and it seems to make sense.

Thank you in advance

Stefano Pieraccini

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