AMBER Archive (2005)

Subject: AMBER: Asking how to creat alanine "dipeptide" in amber8

From: Li Su (suli_at_msu.edu)
Date: Wed May 11 2005 - 10:37:07 CDT

 Sorry to bother. I'm wondering how to creat a structure of alanine
dipeptide in amber. For alanine dipeptide is not a real dipeptide and
actually is N-acetyl-alanine-N'-methylamide, I can't load the correct
structure into amber. I have used INSIGHT II to creat the pdb file for the
alanine dipeptide. But I can not use it directly as the input file for amber
Leap, for it is not composed of regular residues thus some atoms can't be
recognized. And I also tried antechamber, it seemed to me I had to treat the
whole "alanine dipeptide" as a unit, say just like a organic small molecule.
And also if I do this way, I still meet some problem in using the prmtop and
inpcrd files generated this way when launching Sander.
So I'm wonder if somebody knows the situation can reply the email. Thanks a
lot.

Best Wishes,

Li

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