Thank you for the reply. I used that and I defined CSD residue in ffG43a1.rtp file. GROMACS made a .top file but I have got the following error when I run grompp:
processing topology... Generated 279 of the 1225 non-bonded parameter combinations ERROR 0 [file "wt_A.itp", line 11115]: No default Proper Dih. types ERROR 0 [file "wt_A.itp", line 11119]: No default Proper Dih. types Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.386400e+01 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 4516 # G96ANGLES: 6596 # PDIHS: 2363 # IDIHS: 2292 # LJ14: 7108 ------------------------------------------------------- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) ------------------------------------------------------- I would be glad if you help me in this case. Thank you very much. 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: Tuesday, November 6, 2007 10:28:17 PM Subject: Re: [gmx-users] CSDs 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 > [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] > <mailto:[EMAIL PROTECTED]> wrote: > > > >> Send gmx-users mailing list submissions to > >> [email protected] <mailto:[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] <mailto:[EMAIL PROTECTED]> > >> > >> You can reach the person managing the list at > >> [EMAIL PROTECTED] <mailto:[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] <mailto:[EMAIL PROTECTED]>> > >> Subject: [gmx-users] "Specified frame doesn't exist > >> or file not > >> seekable" when using .xtc > >> To: [email protected] <mailto:[email protected]> > >> Message-ID: > >> > >> > > <[EMAIL PROTECTED] > <mailto:[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] > <mailto:[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] <mailto:[email protected]>> > >> Message-ID: <[EMAIL PROTECTED] > <mailto:[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] > <mailto:[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] <mailto:[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] <mailto:[EMAIL PROTECTED]> > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > >> http://folding.bmc.uu.se > >> > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Thu, 1 Nov 2007 16:27:39 +0100 > >> From: "Qiao Baofu" <[EMAIL PROTECTED] <mailto:[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] <mailto:[email protected]>> > >> Message-ID: > >> > >> > > <[EMAIL PROTECTED] > <mailto:[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] <mailto:[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] > <mailto:[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] > <mailto:[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] <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > <mailto:[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] > <mailto:[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 -- 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
