From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Thu Dec 22 2011 - 11:12:10 CST
Dear Norman and Felipe,
Many thanks for your replies.
The problem was indeed the specification of the SCNB and SCEE parts
for oligosaccharides.
By removing them and specifying the related values in the configuration
file, NAMD works fine.
Currently I am simulating the lone saccharide in water, so no problem
in removing
them.
But then I will have to simulate the saccharide together with a protein
and in that case I will need to specify mixed values for SCNB and SCEE
parameters.
Therefore I hope by the time I will be done with the lone glycosaminoglycan,
NAMD will be updated to read those parts in Amber topology files.
Best,
Il 21 dicembre 2011 19:44, felmerino_at_uchile.cl <felmerino_at_uchile.cl> ha scritto:
> Yeah, it is the new part of the topology file added by AmberTools 1.5
> regarding the 1.4 scalings. I had the same problem and you can solve it by
> removing the SCNB and SCEE parts of the topology file by hand. For me it was
> not a problem since i was using the same scalings for all the molecules.
> With glycam i know it is an issue, but up to version 2.8 the program do not
> recognize that part of the topology. Maybe somebody is including it in the
> code?
>
>
>
> felipe
>
> ----Mensaje original----
> De: norman.geist_at_uni-greifswald.de
> Fecha: 21-dic-2011 3:54
> Para: "Norman Geist"<norman.geist_at_uni-greifswald.de>
> CC: "Namd Mailing List"<namd-l_at_ks.uiuc.edu>
> Asunto: AW: namd-l: glycosaminoglycan with GLYCAM06 in amber format
>
>
> 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
>> > >
>> > >
>
>
>
>
-- 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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