Re: glycosaminoglycan with GLYCAM06 in amber format

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Tue Dec 20 2011 - 08:53:59 CST

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

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