AMBER Archive (2008)

Subject: AMBER: neutral C-terminus and N-terminus parameters for amber

From: Lisa Perez (mouse_at_mail.chem.tamu.edu)
Date: Fri May 09 2008 - 12:32:13 CDT

Has anyone developed an amber lib for amino acids with COOH for the
C-terminus and NH2 for the N terminus? I would rather not repeat
this work if it is already out there...

I have a need to perform dynamics calculations on proteins with the C
and N termini in the neutral instead of charged state.
Experimentally, the proteins are subjected to harsh conditions and
forced into the gas phase where they are analyzed via mass
spectrometry. Due to the harsh chemical and gas phase conditions the
charged state of the C and N termini are not know and could be neutral.

Any help would be appreciated.

Thank you,

Lisa Perez

Lisa M. Pérez, Ph.D.
Laboratory for Molecular Simulation, Manager
http://www.chem.tamu.edu/LMS

Texas A&M University
Dept. of Chemistry
P.O. Box 30012
College Station, TX 77842-3012

Chemistry Bldg. RM. 2109
Ofc: (979) 845-9384
Fax: (979) 845-2971

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