AMBER Archive (2004)

Subject: AMBER: cys protecting groups parameters

Date: Fri Jul 09 2004 - 07:41:20 CDT

Hi all,
I'm performing simulations on peptides containing
cystaine residues as they are, but I would like to
try simulating the same peptides when the cysteine
residues are protected by (for example) an
acetamidomethyl group. Unfortunately there are
some missing parameters in the parm99 force field,
regarding the angle bending terms involving the S
atom. Is there any parameter avaible somewhere for
this situation, and what atom tipe schould I chose
for the S atom? Antechamber suggestes the S atom
tipe, and it seems to make sense.
Thank you in advance
Stefano Pieraccini

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