AW: glycosaminoglycan with GLYCAM06 in amber format

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Dec 21 2011 - 00:51:03 CST

It's the file, ccarnal can't read it! Look if you havent't mixed different prep/lib/dat formats between amber versions when building your topology file!

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: Dienstag, 20. Dezember 2011 16:46
> An: Lachele Foley (Lists)
> Cc: Namd Mailing List
> Betreff: Re: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>
> 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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