Re: AW: glycosaminoglycan with GLYCAM06 in amber format

From: felmerino_at_uchile.cl
Date: Wed Dec 21 2011 - 12:44:08 CST

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.deFecha: 21-dic-2011 3:54Para: "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 formatI bet the GLYCAM06 forcefield you use is not amber7 ;)Try build the parm with amber6 tools if you have &amp; 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.> -----Urspr&uuml;ngliche 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.> > > -----Urspr&uuml;ngliche 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.> > >>> > >>> -----Urspr&uuml;ngliche 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.> > >>>>> > >>>>> -----Urspr&uuml;ngliche 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.> > >>>>>>> > >>>>>>> -----Urspr&uuml;ngliche 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 &amp; 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> > >>>>> &amp; 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 &amp;> > >>> 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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