AMBER Archive (2006)

Subject: AMBER: build a polymer with sequence command

From: Shuting Wei (
Date: Fri Sep 22 2006 - 15:41:43 CDT

Dear Amber,

I have to send this again cause i didn't find a solution. Attached
the input file of PAM monomer (prepin, and frcmod)

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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