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AMBER Archive (2006)
Subject: Re: AMBER: Carnal: Internal error: stream file name 2 out of range
From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Aug 23 2006 - 16:16:16 CDT
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It's not clear there is a problem with getting the pdb files
that you want. If the results are ok I wouldn't worry about
the error msg. It looks like carnal is trying to open a
second file, which wasn't specified.
Carnal is being or has been dropped from Amber, so there isn't
any reason to fix cosmetic bugs.
Bill
> I tried to use carnal in amber 8 but i got the following problem in my output:
>
> Carnal: Internal error: stream file name 2 out of range
>
> The input file is:
>
> FILES_IN
> PARM p1 CPL_ACN.prmtop;
> STREAM s1 cpl_maa_cooled_all.pseudo_mdcrd;
> FILES_OUT
> COORD c1 /tmp/temp_mip_pbsa_12692/pdbs.0/pdb PDB;
> DECLARE
> GROUP tpl ( RES 2 );
> CUTRES cr1 tpl 0.05;
> OUTPUT
> COORD c1 s1;
> END
>
> The output file is:
>
>
> - CARNAL -
> AMBER 8.0
>
> COORDINATE ANALYSIS
>
>
> input stdin
> >
> > FILES_IN
> > PARM p1 CPL_ACN.prmtop;
> Reading parm file (CPL_ACN.prmtop)
> parm: opening CPL_ACN.prmtop
> > STREAM s1 cpl_maa_cooled_all.pseudo_mdcrd;
> Using default parm (CPL_ACN.prmtop) for STREAM s1
> (box will be read from stream)
> stream: opening cpl_maa_cooled_all.pseudo_mdcrd
> > FILES_OUT
> > COORD c1 /tmp/temp_mip_pbsa_12692/pdbs.0/pdb PDB;
> > DECLARE
> > GROUP tpl ( RES 2 );
> ** Group tpl: 12 atoms
> > CUTRES cr1 tpl 0.05;
> list of residues at least partially in group:
> 2
> > OUTPUT
> > COORD c1 s1;
> > END
> --CUTRES cr1 130:
> RES 2 2
> --
> starting new coord output file: /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.1
> --CUTRES cr1 130:
> RES 2 2
> --
> starting new coord output file: /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.2
> --CUTRES cr1 130:
> RES 2 2
> --
> .........
> starting new coord output file: /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.1086
> (EOF reached on cpl_maa_cooled_all.pseudo_mdcrd)
> STREAM s1: no more files/crds (iteration 1086)
> SUMMARY
> (EOF reached on cpl_maa_cooled_all.pseudo_mdcrd)
> Internal error: stream file name 2 out of range
>
> What's wrong with it? Any idea? What's stream file name 2?
>
> Thanks in advance,
>
> Shuting Wei
>
>
>
> --=====================_85036405==.ALT
> Content-Type: text/html; charset="us-ascii"
>
> <html>
> <body>
> Dear all,<br><br>
> I tried to use carnal in amber 8 but i got the following problem in my
> output:<br><br>
> Carnal: Internal error: stream file name 2 out of range<br><br>
> The input file is:<br><br>
> <font face="Courier New, Courier" size=2><x-tab>
> </x-tab>FILES_IN<br>
> <x-tab> </x-tab>
> PARM p1 CPL_ACN.prmtop;<br>
> <x-tab> </x-tab>STREAM s1
> cpl_maa_cooled_all.pseudo_mdcrd;<br>
> <x-tab> </x-tab>
> FILES_OUT<br>
> <x-tab> </x-tab>
> COORD c1 /tmp/temp_mip_pbsa_12692/pdbs.0/pdb PDB;<br>
> <x-tab> </x-tab>DECLARE<br>
> <x-tab> </x-tab>
> GROUP tpl ( RES 2 );<br>
> <x-tab> </x-tab>CUTRES cr1
> tpl 0.05;<br>
> <x-tab> </x-tab>OUTPUT<br>
> <x-tab> </x-tab>
> COORD c1 s1;<br>
> <x-tab> </x-tab>END<br><br>
> The output file is:<br><br>
> <br>
> <x-tab> </x-tab><x-tab>
> </x-tab><x-tab>
> </x-tab> - CARNAL
> -<br>
> <x-tab> </x-tab><x-tab>
> </x-tab><x-tab>
> </x-tab>
> AMBER 8.0<br><br>
> <x-tab> </x-tab><x-tab>
> </x-tab>
> COORDINATE ANALYSIS<br><br>
> <br>
> input stdin <br>
> > <br>
> > <x-tab> </x-tab>FILES_IN<br>
> >
> <x-tab> </x-tab>
> PARM p1 CPL_ACN.prmtop;<br>
> Reading parm file (CPL_ACN.prmtop)<br>
> parm: opening CPL_ACN.prmtop<br>
> > <x-tab> </x-tab>STREAM s1
> cpl_maa_cooled_all.pseudo_mdcrd;<br>
> Using default parm (CPL_ACN.prmtop) for STREAM s1<br>
> (box will be read from stream)<br>
> stream: opening cpl_maa_cooled_all.pseudo_mdcrd<br>
> > <x-tab> </x-tab>FILES_OUT<br>
> >
> <x-tab> </x-tab>
> COORD c1 /tmp/temp_mip_pbsa_12692/pdbs.0/pdb PDB;<br>
> > <x-tab> </x-tab>DECLARE<br>
> >
> <x-tab> </x-tab>
> GROUP tpl ( RES 2 );<br>
> ** Group tpl: 12 atoms<br>
> > <x-tab> </x-tab>CUTRES cr1 tpl
> 0.05;<br>
> list of residues at least partially in group:<br>
> <x-tab> </x-tab>2 <br>
> > <x-tab> </x-tab>OUTPUT<br>
> >
> <x-tab> </x-tab>
> COORD c1 s1;<br>
> > <x-tab> </x-tab>END<br>
> --CUTRES cr1 130:<br>
> RES 2 2<br>
> --<br>
> starting new coord output file:
> /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.1<br>
> --CUTRES cr1 130:<br>
> RES 2 2<br>
> --<br>
> starting new coord output file:
> /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.2<br>
> --CUTRES cr1 130:<br>
> RES 2 2<br>
> --<br>
> .........<br>
> starting new coord output file:
> /tmp/temp_mip_pbsa_12692/pdbs.0/pdb.1086<br>
> (EOF reached on cpl_maa_cooled_all.pseudo_mdcrd)<br>
> STREAM s1: no more files/crds (iteration 1086)<br>
> SUMMARY<br>
> (EOF reached on cpl_maa_cooled_all.pseudo_mdcrd)<br>
> <b>Internal error: stream file name 2 out of range<br><br>
> </b>What's wrong with it? Any idea? What's stream file name 2?<br><br>
> Thanks in advance,<br><br>
> Shuting Wei<br><br>
> <br>
> <x-tab> </x-tab></font>
> </body>
> </html>
>
> --=====================_85036405==.ALT--
>
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- Next message: David A. Case: "Re: AMBER: 0 steps the same as 1 step?"
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