From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Tue Dec 20 2011 - 08:55:58 CST
Hello there,
The files come directly out of tleap and they work perfectly
with sander and pmemd (I tested minimisation, heating, NPT equilibration
and NVT production run).
I used AmberTools1.5, with all the bugfixes applied.
Moreover I downloaded the latest version of GLYCAM06 ff
from the related website.
I don't really know what is wrong with NAMD in this case.
Best,
Il 20 dicembre 2011 12:45, Norman Geist
<norman.geist_at_uni-greifswald.de> ha scritto:
> 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
>
>
-- 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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