<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><h2>3-sulfinoalanine</h2><div> </div>Jahanshah Ashkani,<br>PhD student of Biotechnology & Genetics,<br>University of the Western Cape,<br>Biotechnology Department,<br>Private Bag X17,<br>7735 Bellville,<br>Cape Town,<br>South Africa<br>jashkani@mail.biotech.uwc.ac.za<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: David van der Spoel <spoel@xray.bmc.uu.se><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Thursday, November 1, 2007 8:38:59 PM<br>Subject: Re: [gmx-users] CSDs<br><br>syawash Rezaei wrote:<br>> Hi there,<br>> I would be glad if you let me know how can I use a<br>> pdb
file with CSDs in GROMACS.<br><br>and what might that be?<br><br>> Thank you very much.<br>> --- <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:<br>> <br>>> Send gmx-users mailing list submissions to<br>>> <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>><br>>> To subscribe or unsubscribe via the World Wide Web,<br>>> visit<br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>> or, via email, send a message with subject or body<br>>> 'help' to<br>>> <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>><br>>>
You can reach the person managing the list at<br>>> <a ymailto="mailto:gmx-users-owner@gromacs.org" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>>><br>>> When replying, please edit your Subject line so it<br>>> is more specific<br>>> than "Re: Contents of gmx-users digest..."<br>>><br>>><br>>> Today's Topics:<br>>><br>>> 1. "Specified frame doesn't exist or file not<br>>> seekable" when<br>>> using .xtc (Qiao Baofu)<br>>> 2. Re: "Specified frame doesn't exist or file not<br>>> seekable" when<br>>> using .xtc (David van der Spoel)<br>>> 3. Re: "Specified frame doesn't exist or file not<br>>> seekable" when<br>>> using .xtc (Qiao
Baofu)<br>>> 4. Re: "Specified frame doesn't exist or file not<br>>> seekable" when<br>>> using .xtc (David van der Spoel)<br>>> 5. *.gro output file being written to inverse<br>>> (Luciano Costa)<br>>> 6. mdrun 3.3.2 crash - gmx_sumi called in serial<br>>> run with RF<br>>> (Michel Cuendet)<br>>><br>>><br>>><br>>
----------------------------------------------------------------------<br>>> Message: 1<br>>> Date: Thu, 1 Nov 2007 16:17:32 +0100<br>>> From: "Qiao Baofu" <<a ymailto="mailto:qiaobf@gmail.com" href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>><br>>> Subject: [gmx-users] "Specified frame doesn't exist<br>>> or file not<br>>> seekable" when using .xtc<br>>> To: <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> Message-ID:<br>>><br>>><br>> <<a ymailto="mailto:6a91f07b0711010817wb3e9454j7145001c33e8449d@mail.gmail.com" href="mailto:6a91f07b0711010817wb3e9454j7145001c33e8449d@mail.gmail.com">6a91f07b0711010817wb3e9454j7145001c33e8449d@mail.gmail.com</a>><br>>> Content-Type: text/plain; charset="iso-8859-1"<br>>><br>>> Hi, all<br>>><br>>> When I using the
.xtc file to analyse, I always meet<br>>> the following error<br>>> information<br>>> Specified frame doesn't exist or file not seekable<br>>> While it works when using the .trr file. In<br>>> analyzing, only the coordinate<br>>> is used. Therefore, I want to use .xtc file. In this<br>>> way, it runs a little<br>>> faster. However, the above proble exits. What's<br>>> wrong with the .xtc file?<br>>> and how to solve it?<br>>><br>>> Thanks!<br>>><br>>> -- <br>>> Sincerely yours,<br>>> Dr. Baofu Qiao<br>>> -------------- next part --------------<br>>> An HTML attachment was scrubbed...<br>>> URL:<br>>><br>>
<a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20071101/dff744c6/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20071101/dff744c6/attachment-0001.html</a><br>>> ------------------------------<br>>><br>>> Message: 2<br>>> Date: Thu, 01 Nov 2007 16:19:29 +0100<br>>> From: David van der Spoel <<a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>>> Subject: Re: [gmx-users] "Specified frame doesn't<br>>> exist or file not<br>>> seekable" when using .xtc<br>>> To: Discussion list for GROMACS users<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>> Message-ID: <<a ymailto="mailto:4729EE81.5010704@xray.bmc.uu.se"
href="mailto:4729EE81.5010704@xray.bmc.uu.se">4729EE81.5010704@xray.bmc.uu.se</a>><br>>> Content-Type: text/plain; charset=ISO-8859-1;<br>>> format=flowed<br>>><br>>> Qiao Baofu wrote:<br>>>> Hi, all<br>>>><br>>>> When I using the .xtc file to analyse, I always<br>>> meet the following error <br>>>> information<br>>>> Specified frame doesn't exist or file not<br>>> seekable<br>>>> While it works when using the .trr file. In<br>>> analyzing, only the <br>>>> coordinate is used. Therefore, I want to use .xtc<br>>> file. In this way, it <br>>>> runs a little faster. However, the above proble<br>>> exits. What's wrong <br>>>> with the .xtc file? and how to solve it?<br>>>><br>>> gmx version please.<br>>>> Thanks!<br>>>><br>>>> -- <br>>>> Sincerely
yours,<br>>>> Dr. Baofu Qiao<br>>>><br>>>><br>>>><br>>
------------------------------------------------------------------------<br>>>> _______________________________________________<br>>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>>>> Please don't post (un)subscribe requests to the<br>>> list. Use the <br>>>> www interface or send it to<br>>> <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>>> Can't post? Read<br>>> <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>>><br>>><br>>> -- <br>>> David van der Spoel, Ph.D.<br>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol.,<br>>> Uppsala University.<br>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>>> Fax: +4618511755.<br>>> <a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a ymailto="mailto:spoel@gromacs.org" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <br>>> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>>><br>>><br>>> ------------------------------<br>>><br>>> Message: 3<br>>> Date: Thu, 1 Nov 2007 16:27:39 +0100<br>>> From: "Qiao Baofu" <<a ymailto="mailto:qiaobf@gmail.com"
href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>><br>>> Subject: Re: [gmx-users] "Specified frame doesn't<br>>> exist or file not<br>>> seekable" when using .xtc<br>>> To: "Discussion list for GROMACS users"<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>> Message-ID:<br>>><br>>><br>> <<a ymailto="mailto:6a91f07b0711010827y4611ed4ej309e0ebf5c67daed@mail.gmail.com" href="mailto:6a91f07b0711010827y4611ed4ej309e0ebf5c67daed@mail.gmail.com">6a91f07b0711010827y4611ed4ej309e0ebf5c67daed@mail.gmail.com</a>><br>>> Content-Type: text/plain; charset="iso-8859-1"<br>>><br>>> Hi,<br>>><br>>> I am using Gromacs 3.3.1. The .xtc file is obtained<br>>> from mdrun, as shown in<br>>> the following<br>>><br>>> ; OUTPUT CONTROL
OPTIONS<br>>> ; Output frequency for coords (x), velocities (v)<br>>> and forces (f)<br>>> nstxout = 0<br>>> nstvout = 0<br>>> nstfout = 0<br>>> ; Checkpointing helps you continue after crashes<br>>> nstcheckpoint = 0<br>>> ; Output frequency for energies to log file and<br>>> energy file<br>>> nstlog = 1000<br>>> nstenergy = 100<br>>> ; Output frequency and precision for xtc file<br>>> nstxtcout = 10<br>>> xtc-precision =
1000<br>>><br>>><br>>><br>>><br>>><br>>> 2007/11/1, David van der Spoel<br>>> <<a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:<br>>>> Qiao Baofu wrote:<br>>>>> Hi, all<br>>>>><br>>>>> When I using the .xtc file to analyse, I always<br>>> meet the following error<br>>>>> information<br>>>>> Specified frame doesn't exist or file not<br>>> seekable<br>>>>> While it works when using the .trr file. In<br>>> analyzing, only the<br>>>>> coordinate is used. Therefore, I want to use<br>>> .xtc file. In this way, it<br>>>>> runs a little faster. However, the above proble<br>>> exits. What's wrong<br>>>>> with the .xtc file? and how to solve it?<br>>>>><br>> === message truncated ===<br>>
<br>> <br>> __________________________________________________<br>> Do You Yahoo!?<br>> Tired of spam? Yahoo! Mail has the best spam protection around <br>> <a href="http://mail.yahoo.com" target="_blank">http://mail.yahoo.com</a> <br>> <br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before
posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>-- <br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
+4618511755.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a ymailto="mailto:spoel@gromacs.org" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before
posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div><br></div></div><br>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com </body></html>