[gmx-users] CSDs

jahanshah ashkani ashkani_2003 at yahoo.com
Tue Nov 6 21:18:30 CET 2007


3-sulfinoalanine 
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 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>
>> Subject: [gmx-users] "Specified frame doesn't exist
>> or file not
>>     seekable"    when using .xtc
>> To: gmx-users at gromacs.org
>> Message-ID:
>>
>>
> <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>
>> 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>
>> Message-ID: <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
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>>> Please search the archive at
>> http://www.gromacs.org/search before posting!
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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
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 1 Nov 2007 16:27:39 +0100
>> From: "Qiao Baofu" <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>
>> Message-ID:
>>
>>
> <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>:
>>> 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    spoel at gromacs.org   http://folding.bmc.uu.se
_______________________________________________
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