From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Mon Dec 19 2011 - 05:04:40 CST
Hi Norman,
You are right: "filename" name was simply put by me, just for posting the
issue here. My parm7 file has actually a different name.
Hence the problem must be in the file itself, but I have generated it
with the latest version of tleap (AmberTools1.5) with all the bugfixes applied.
Moreover the files (coordinates and parameter) work perfectly with
Amber10 software package, that is why I am puzzled about this.
I would really appreciate any further thought.
Best,
Il 19 dicembre 2011 06:45, Norman Geist
<norman.geist_at_uni-greifswald.de> ha scritto:
> 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
>
>
-- 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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