[gmx-users] CSDs

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 6 21:28:17 CET 2007


jahanshah ashkani wrote:
> 
> 
> 
>     3-sulfinoalanine

please try prodrg, but you probably have to compute charges in some oe 
another too. read literature!
> 
>  
> Jahanshah Ashkani,
> PhD student of Biotechnology & Genetics,
> University of the Western Cape,
> Biotechnology Department,
> Private Bag X17,
> 7735 Bellville,
> Cape Town,
> South Africa
> jashkani at mail.biotech.uwc.ac.za
> 
> 
> ----- Original Message ----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, November 1, 2007 8:38:59 PM
> Subject: Re: [gmx-users] CSDs
> 
> syawash Rezaei wrote:
>  > Hi there,
>  >  I would be glad if you let me know how can I use a
>  > pdb file with CSDs in GROMACS.
> 
> and what might that be?
> 
>  >  Thank you very much.
>  > --- gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org> wrote:
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>  >> Today's Topics:
>  >>
>  >>    1. "Specified frame doesn't exist or file not
>  >> seekable"    when
>  >>      using .xtc (Qiao Baofu)
>  >>    2. Re: "Specified frame doesn't exist or file not
>  >> seekable"    when
>  >>      using .xtc (David van der Spoel)
>  >>    3. Re: "Specified frame doesn't exist or file not
>  >> seekable"    when
>  >>      using .xtc (Qiao Baofu)
>  >>    4. Re: "Specified frame doesn't exist or file not
>  >> seekable"    when
>  >>      using .xtc (David van der Spoel)
>  >>    5. *.gro output file being written to inverse
>  >> (Luciano Costa)
>  >>    6. mdrun 3.3.2 crash - gmx_sumi called in serial
>  >> run with    RF
>  >>      (Michel Cuendet)
>  >>
>  >>
>  >>
>  > ----------------------------------------------------------------------
>  >> Message: 1
>  >> Date: Thu, 1 Nov 2007 16:17:32 +0100
>  >> From: "Qiao Baofu" <qiaobf at gmail.com <mailto:qiaobf at gmail.com>>
>  >> Subject: [gmx-users] "Specified frame doesn't exist
>  >> or file not
>  >>     seekable"    when using .xtc
>  >> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>  >> Message-ID:
>  >>
>  >>
>  > <6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com 
> <mailto:6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com>>
>  >> Content-Type: text/plain; charset="iso-8859-1"
>  >>
>  >> Hi, all
>  >>
>  >> When I using the .xtc file to analyse, I always meet
>  >> the following error
>  >> information
>  >>  Specified frame doesn't exist or file not seekable
>  >> While it works when using the .trr file. In
>  >> analyzing, only the coordinate
>  >> is used. Therefore, I want to use .xtc file. In this
>  >> way, it runs a little
>  >> faster. However, the above proble exits.  What's
>  >> wrong with the .xtc file?
>  >> and how to solve it?
>  >>
>  >> Thanks!
>  >>
>  >> --
>  >> Sincerely yours,
>  >> Dr. Baofu Qiao
>  >> -------------- next part --------------
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>  >> ------------------------------
>  >>
>  >> Message: 2
>  >> Date: Thu, 01 Nov 2007 16:19:29 +0100
>  >> From: David van der Spoel <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>>
>  >> Subject: Re: [gmx-users] "Specified frame doesn't
>  >> exist or file not
>  >>     seekable"    when using .xtc
>  >> To: Discussion list for GROMACS users
>  >> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  >> Message-ID: <4729EE81.5010704 at xray.bmc.uu.se 
> <mailto:4729EE81.5010704 at xray.bmc.uu.se>>
>  >> Content-Type: text/plain; charset=ISO-8859-1;
>  >> format=flowed
>  >>
>  >> Qiao Baofu wrote:
>  >>> Hi, all
>  >>>
>  >>> When I using the .xtc file to analyse, I always
>  >> meet the following error
>  >>> information
>  >>>  Specified frame doesn't exist or file not
>  >> seekable
>  >>> While it works when using the .trr file. In
>  >> analyzing, only the
>  >>> coordinate is used. Therefore, I want to use .xtc
>  >> file. In this way, it
>  >>> runs a little faster. However, the above proble
>  >> exits.  What's wrong
>  >>> with the .xtc file? and how to solve it?
>  >>>
>  >> gmx version please.
>  >>> Thanks!
>  >>>
>  >>> --
>  >>> Sincerely yours,
>  >>> Dr. Baofu Qiao
>  >>>
>  >>>
>  >>>
>  > ------------------------------------------------------------------------
>  >>> _______________________________________________
>  >>> gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
>  >>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>  >>
>  >>
>  >> --
>  >> David van der Spoel, Ph.D.
>  >> Molec. Biophys. group, Dept. of Cell & Molec. Biol.,
>  >> Uppsala University.
>  >> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>  >> Fax: +4618511755.
>  >> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>    
> spoel at gromacs.org <mailto:spoel at gromacs.org> 
>  >> http://folding.bmc.uu.se
>  >>
>  >>
>  >> ------------------------------
>  >>
>  >> Message: 3
>  >> Date: Thu, 1 Nov 2007 16:27:39 +0100
>  >> From: "Qiao Baofu" <qiaobf at gmail.com <mailto:qiaobf at gmail.com>>
>  >> Subject: Re: [gmx-users] "Specified frame doesn't
>  >> exist or file not
>  >>     seekable"    when using .xtc
>  >> To: "Discussion list for GROMACS users"
>  >> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  >> Message-ID:
>  >>
>  >>
>  > <6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com 
> <mailto:6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com>>
>  >> Content-Type: text/plain; charset="iso-8859-1"
>  >>
>  >> Hi,
>  >>
>  >> I am using Gromacs 3.3.1.  The .xtc file is obtained
>  >> from mdrun, as shown in
>  >> the following
>  >>
>  >> ; OUTPUT CONTROL OPTIONS
>  >> ; Output frequency for coords (x), velocities (v)
>  >> and forces (f)
>  >> nstxout                  = 0
>  >> nstvout                  = 0
>  >> nstfout                  = 0
>  >> ; Checkpointing helps you continue after crashes
>  >> nstcheckpoint            = 0
>  >> ; Output frequency for energies to log file and
>  >> energy file
>  >> nstlog                  = 1000
>  >> nstenergy                = 100
>  >> ; Output frequency and precision for xtc file
>  >> nstxtcout                = 10
>  >> xtc-precision            = 1000
>  >>
>  >>
>  >>
>  >>
>  >>
>  >> 2007/11/1, David van der Spoel
>  >> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>:
>  >>> Qiao Baofu wrote:
>  >>>> Hi, all
>  >>>>
>  >>>> When I using the .xtc file to analyse, I always
>  >> meet the following error
>  >>>> information
>  >>>>  Specified frame doesn't exist or file not
>  >> seekable
>  >>>> While it works when using the .trr file. In
>  >> analyzing, only the
>  >>>> coordinate is used. Therefore, I want to use
>  >> .xtc file. In this way, it
>  >>>> runs a little faster. However, the above proble
>  >> exits.  What's wrong
>  >>>> with the .xtc file? and how to solve it?
>  >>>>
>  > === message truncated ===
>  >
>  >
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> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org 
> <mailto:spoel at gromacs.org>  http://folding.bmc.uu.se
> _______________________________________________
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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