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 [EMAIL PROTECTED]
----- Original Message ---- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> 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. > --- [EMAIL PROTECTED] wrote: > >> Send gmx-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, >> visit >> http://www.gromacs.org/mailman/listinfo/gmx-users >> or, via email, send a message with subject or body >> 'help' to >> [EMAIL PROTECTED] >> >> You can reach the person managing the list at >> [EMAIL PROTECTED] >> >> When replying, please edit your Subject line so it >> is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> 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" <[EMAIL PROTECTED]> >> Subject: [gmx-users] "Specified frame doesn't exist >> or file not >> seekable" when using .xtc >> To: [email protected] >> Message-ID: >> >> > <[EMAIL PROTECTED]> >> 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 -------------- >> An HTML attachment was scrubbed... >> URL: >> > http://www.gromacs.org/pipermail/gmx-users/attachments/20071101/dff744c6/attachment-0001.html >> ------------------------------ >> >> Message: 2 >> Date: Thu, 01 Nov 2007 16:19:29 +0100 >> From: David van der Spoel <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] "Specified frame doesn't >> exist or file not >> seekable" when using .xtc >> To: Discussion list for GROMACS users >> <[email protected]> >> Message-ID: <[EMAIL PROTECTED]> >> 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 [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >> http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the >> list. Use the >>> www interface or send it to >> [EMAIL PROTECTED] >>> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- >> 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. >> [EMAIL PROTECTED] [EMAIL PROTECTED] >> http://folding.bmc.uu.se >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 1 Nov 2007 16:27:39 +0100 >> From: "Qiao Baofu" <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] "Specified frame doesn't >> exist or file not >> seekable" when using .xtc >> To: "Discussion list for GROMACS users" >> <[email protected]> >> Message-ID: >> >> > <[EMAIL PROTECTED]> >> 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 >> <[EMAIL PROTECTED]>: >>> 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 === > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
