AMBER Archive (2009)

Subject: [AMBER] ambertools for NAMD

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Thu May 07 2009 - 07:35:24 CDT

Hi all,

I am trying to run a MD simulation using NAMD but ht eamber force field but
I get an error message when trying to run the input file

Reading parm file (fr.prmtop) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 350 H-H bonds.
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN PARAMETER FILES
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN
PARAMETER FILES

Charm++ fatal error:
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND HW - HW IN PARAMETER FILES

Abort

I know that there has been a bug but it should be fixed in the NAMD 2.7b1
version - I have looked into the *.prmtop file and I find the HW in %FLAG
AMBER_ATOM_TYPE
%FORMAT(20a4)

section but then I don't find it anymore in any of the other sections. Any
suggestions or hints how to solve the problem or debug the parameter file?

Thanks in advance

Best
J
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber