AW: glycosaminoglycan with GLYCAM06 in amber format

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 20 2011 - 06:45:32 CST

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

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