AW: glycosaminoglycan with GLYCAM06 in amber format

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Dec 19 2011 - 07:35:58 CST

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

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