<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">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:<br><br>processing topology...<br>Generated 279 of the 1225 non-bonded parameter combinations<br>ERROR 0 [file "wt_A.itp", line 11115]:<br> No default Proper Dih. types<br>ERROR 0 [file "wt_A.itp", line 11119]:<br> No default Proper Dih. types<br>Excluding 3 bonded neighbours for Protein_A 1<br>Excluding 3 bonded neighbours for Protein_B 1<br>NOTE:<br> System has non-zero total charge: -1.386400e+01<br><br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering
atomtypes...<br>converting bonded parameters...<br># G96BONDS: 4516<br># G96ANGLES: 6596<br># PDIHS: 2363<br># IDIHS: 2292<br># LJ14: 7108<br><br>-------------------------------------------------------<br>Program grompp, VERSION 3.3.2<br>Source code file: grompp.c, line: 1182<br><br>Fatal error:<br>There were 2 errors in input file(s)<br>-------------------------------------------------------<br><br>I would be glad if you help me in this case.<br>Thank you very much.<br><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: Tuesday, November 6, 2007 10:28:17 PM<br>Subject: Re: [gmx-users] CSDs<br><br>jahanshah ashkani wrote:<br>> <br>> <br>> <br>> 3-sulfinoalanine<br><br>please try prodrg, but you probably have to compute charges in some oe <br>another too. read literature!<br>> <br>> <br>> 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>> <a ymailto="mailto:jashkani@mail.biotech.uwc.ac.za"
href="mailto:jashkani@mail.biotech.uwc.ac.za">jashkani@mail.biotech.uwc.ac.za</a><br>> <br>> <br>> ----- Original Message ----<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>> To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><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>
<br>> <mailto:<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> <mailto:<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>
<mailto:<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>
<mailto:<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> <mailto:<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> <mailto:<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>> <mailto:<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>> > <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>> <mailto:<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> <mailto:<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>> <mailto:<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>> <mailto:<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>
<mailto:<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> <mailto:<a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>
<br>> <a ymailto="mailto:spoel@gromacs.org" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <mailto:<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> <mailto:<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> <mailto:<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>> <mailto:<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> <mailto:<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>> <mailto:<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 <br>> 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>> <mailto:<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> <mailto:<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>> <mailto:<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>> <mailto:<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>> <mailto:<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>> 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>>
------------------------------------------------------------------------<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
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