AMBER Archive (2006)

Subject: AMBER: Building polymer with sequence command

From: gtg549i_at_mail.gatech.edu
Date: Thu Oct 05 2006 - 11:46:11 CDT

Hi, Dear Amber Users,

I tried to use sequence to build a polymer structure in leap. Here is the
error message:

xleap
-I: Adding /usr/local/amber9/dat/leap/prep to search path.
-I: Adding /usr/local/amber9/dat/leap/lib to search path.
-I: Adding /usr/local/amber9/dat/leap/parm to search path.
-I: Adding /usr/local/amber9/dat/leap/cmd to search path.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C2 from PAM did not match !
!
!ABORTING.

Attached my leap.log and prepin file. PAM [CH3CH(OH)CH2N(CH3)2] is the unit i
want to connect together to form a polymer chain. Do i need to use
CH3CH(OH)CH2N(CH3)2 or CH2CH(OH)CH2N+(CH3)2 as unit to build the polymer? I am
thinking the problem may due to the N atom, it needs to be charged after
connecting to the other unit. Any suggestion for this problem? Thanks a lot!

Shuting




-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu