glycosaminoglycan with GLYCAM06 in amber format

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Sun Dec 18 2011 - 10:44:48 CST

Dear NAMD users and developers,

I am trying to simulate a glycosaminoglycan (GAG) molecule in water
using GLYCAM06 force field.

The topology/parameters and coordinates files I am implementing are in Amber
format (filename.parm7 and filename.crd).

Soon, in attempting to minimise the system, I get the following error:

#########################################################
Reading parm file (filename.parm7) ...
PARM file in AMBER 7 format
FATAL ERROR: Failed to read AMBER parm file!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Failed to read AMBER parm file!

[0] Stack Traceback:
  [0:0] CmiAbort+0x7b [0xbf1bd9]
  [0:1] _Z8NAMD_diePKc+0x62 [0x535542]
  [0:2] _ZN9NamdState14configListInitEP10ConfigList+0xcb4 [0x9fc42a]
  [0:3] _ZN9ScriptTcl9initcheckEv+0x5e [0xa7c342]
  [0:4] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0xa78a94]
  [0:5] TclInvokeStringCommand+0x91 [0xc26a58]
  [0:6] /home/max/NAMD/NAMD_2.8_Linux-x86_64/namd2 [0xc5c8a8]
  [0:7] Tcl_EvalEx+0x176 [0xc5ceeb]
  [0:8] Tcl_EvalFile+0x134 [0xc548f4]
  [0:9] _ZN9ScriptTcl4loadEPc+0x10 [0xa77e42]
  [0:10] _Z18after_backend_initiPPc+0x448 [0x539cc8]
  [0:11] main+0x3a [0x53984a]
  [0:12] __libc_start_main+0xfd [0x7f0a4a077a7d]
  [0:13] _ZNSt8ios_base4InitD1Ev+0x4a [0x534e3a]
Fatal error on PE 0> FATAL ERROR: Failed to read AMBER parm file!
###############################################################

Any suggestion or hints about this would be really appreciated.

I should add that both files work fine with Amber software, hence
I assume they do not contain errors.

Many thanks in advance.

All the best,

-- 
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini_at_ed.ac.uk
             mozz76_at_gmail.com
             maxp_at_iesl.forth.gr

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