AMBER Archive (2002)

Subject: transferring structures

From: Matt Hartings (mhartings_at_yahoo.com)
Date: Wed Jun 26 2002 - 12:24:23 CDT

I am currently trying to transfer a peptide structure
that I generated using a different suite of programs
to Amber. It seems to be having troubles with the
acetyl group. I even have troubles inputing structures
with acetyl groups directly from programs like
HyperChem. The amber prompt gives me errors in the
LEap prompt. When I try to loadpdb, it says that it my
structures have missing atoms which it adds. It then
will not save the parameters when I use the
saveAmberParm command. I have tried some of the
tutorials with pdb's from Brookhaven and they seem to
work out alright. I have even gotten a simple
minimization to work out when I use un-acetylated
peptides generated with Hyperchem. Its only with the
acetylated peptides that I am experiencing problems.
I would greatly appreciate a response. If you need
more information from me, please let me know.
Thank you
Matt Hartings
Northwestern University

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