AW: glycosaminoglycan with GLYCAM06 in amber format

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Dec 21 2011 - 00:54:50 CST

I bet the GLYCAM06 forcefield you use is not amber7 ;)
Try build the parm with amber6 tools if you have & there must be a converting tool for amber7 oldparmnewparm or something like that. Or look what changed in the format from amber6 to 7 and look your lib/prep/dat or what you use.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> Gesendet: Mittwoch, 21. Dezember 2011 07:51
> An: 'Massimiliano Porrini'
> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
> Betreff: AW: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>
> 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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