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

From: Li Su <>
Date: Wed, 11 May 2005 11:37:07 -0400

 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

Best Wishes,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed May 11 2005 - 16:53:01 PDT
Custom Search