AMBER: the sequence command in leap

From: Shuting Wei <>
Date: Wed, 20 Sep 2006 11:32:17 -0400

Dear Amber,

I tried to build a polymer chain in leap with sequence command, but i
got the following error:

> loadamberprep polyamine.prepin
Loading Prep file: ./polyamine.prepin
> loadamberparams polyamine.frcmod
Loading parameters: ./polyamine.frcmod
Reading force field mod type file (frcmod)
> set PAM tail PAM.1.12
> desc PAM
UNIT name: PAM
Head atom: .R<PAM 1>.A<C1 1>
Tail atom: .R<PAM 1>.A<N4 12>
R<PAM 1>
> triPAM = sequence { PAM PAM PAM }
ERROR: Comparing atoms N4, H14, H16, H18 to atoms C2, N4, H18, H14
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 121
!FATAL: Message: Atom C2 is not in the first list

What's wrong with my input? Thanks a lot!


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Received on Sun Sep 24 2006 - 06:07:04 PDT
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