AW: glycosaminoglycan with GLYCAM06 in amber format

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Dec 19 2011 - 00:45:19 CST

Hi,

make sure that the parameter "parmfile xx.parm7" points to the right file.
>From your output attached it seems that namd is trying to open a file called
"filename.parm7". I can't imagine that your file is called like that.

If namd tries to read the right file, then there could be something wrong
with the parmfile. You should rebuild it with your corresponding tool. We
usually use leap for that.

Let me know.

Good luck

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Massimiliano Porrini
> Gesendet: Sonntag, 18. Dezember 2011 17:45
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>
> 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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