Re: glycosaminoglycan with GLYCAM06 in amber format

From: Massimiliano Porrini (mozz76_at_gmail.com)
Date: Tue Dec 20 2011 - 09:46:18 CST

Hi,

Honestly I feared the issue was
about SCEE and SCNB.

I am currently using NAMD 2.8, I wonder
if I used the latest version, the problem
would persist.

I will give a try though.

Cheers,

Sent from my iPhone

On Dec 20, 2011, at 15:53, "Lachele Foley (Lists)" <lf.list_at_gmail.com> wrote:

> Hi...
>
> I don't know much about namd. But, I know a bit about Glycam. I have
> heard that namd has trouble reading the new SCEE and SCNB portions of
> the topology file. Leap now inserts those fields by default, as they
> are now required in Amber. Could that be the problem?
>
> :-) Lachele
>
>
> On Tue, Dec 20, 2011 at 7:45 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
>> Hi,
>>
>> I could reproduce your error, so it's probably not a problem of your namd
>> installation. I tried reading the top/crd with ccarnal and it wasn't also
>> able to read it correctly. The error ccarnal threw pointed to a misreading,
>> maybe due to wrong format version. Have you used a converting tool or does
>> this file come directly out of leap??
>>
>> Have you tried reading the files with sander/pmemd? What version of
>> ambertools do you use?
>>
>> Definitely the parm is not in a correct parm7 format as it seems.
>>
>>
>> Good luck
>>
>> Norman Geist.
>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: mozz76_at_gmail.com [mailto:mozz76_at_gmail.com] Im Auftrag von
>>> Massimiliano Porrini
>>> Gesendet: Dienstag, 20. Dezember 2011 10:45
>>> An: Norman Geist
>>> Cc: Namd Mailing List
>>> Betreff: Re: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>>>
>>> Dear Norman,
>>>
>>> Thanks for the reply.
>>>
>>> I have tried what you suggested and the message is the same, apart from
>>> few lines regarding the attempt to uncompress a prospective compressed
>>> parm file (I changed the filename into test_H2O.parm7):
>>>
>>> ##############################################
>>> Reading parm file (test_H2O.parm7) ...
>>> Command = zcat test_H2O.parm7.Z
>>> Filename.Z = test_H2O.parm7.Z
>>> Command = gzip -d -c test_H2O.parm7.gz
>>> Filename.gz = test_H2O.parm7.gz
>>> 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 [0x7fde98ac2a7d]
>>> [0:13] _ZNSt8ios_base4InitD1Ev+0x4a [0x534e3a] Fatal error on PE 0>
>>> FATAL ERROR: Failed to read AMBER parm file!
>>> ###############################################################
>>>
>>> Hereby I also attached all the files I am using, It would be great if
>>> we can get this issue sorted out.
>>>
>>> Thanks in advance and all the best.
>>>
>>>
>>> Il 19 dicembre 2011 13:35, Norman Geist
>>> <norman.geist_at_uni-greifswald.de> ha scritto:
>>>> Hi,
>>>>
>>>> that's what I figured. ^^
>>>>
>>>> It sounds a bit like an configuration problem. I don't know if namd
>>>> would bring a message about no such file if it wouldn't find the top,
>>>> but you could try to change the filename in the config and see. If
>>>> namd shows another message then, it really claims about the file
>>>> format, if the message is the same, it doesn't find the file.
>>>>
>>>> Please attach a link to your top,crd,namd.in
>>>>
>>>> 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: Montag, 19. Dezember 2011 12:05
>>>>> An: Norman Geist
>>>>> Cc: Namd Mailing List
>>>>> Betreff: Re: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>>>>>
>>>>> 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
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>>
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
>

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