[gmx-users] CSDs
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 6 21:46:35 CET 2007
jahanshah ashkani wrote:
>
> 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:
>
read chapter 5 of the manual and check the wiki. all info is there.
> 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
> 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: 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
> > jashkani at mail.biotech.uwc.ac.za <mailto:jashkani at mail.biotech.uwc.ac.za>
> >
> >
> > ----- Original Message ----
> > From: David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto: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
> <mailto:gmx-users-request at gromacs.org>
> > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> wrote:
> > >
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> > >> 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" <qiaobf at gmail.com <mailto:qiaobf at gmail.com>
> <mailto:qiaobf at gmail.com <mailto: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 <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > >> Message-ID:
> > >>
> > >>
> > > <6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com
> <mailto:6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com>
> > <mailto:6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com
> <mailto: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 --------------
> > >> 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 <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>
> > <mailto:spoel at xray.bmc.uu.se <mailto: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 <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
> > >> Message-ID: <4729EE81.5010704 at xray.bmc.uu.se
> <mailto:4729EE81.5010704 at xray.bmc.uu.se>
> > <mailto:4729EE81.5010704 at xray.bmc.uu.se
> <mailto: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
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > >>> 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
> > >> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> > >>> 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.
> > >> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> > spoel at gromacs.org <mailto:spoel at gromacs.org>
> <mailto:spoel at gromacs.org <mailto: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 <mailto:qiaobf at gmail.com>
> <mailto:qiaobf at gmail.com <mailto: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 <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
> > >> Message-ID:
> > >>
> > >>
> > > <6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com
> <mailto:6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com>
> > <mailto:6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com
> <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> spoel at gromacs.org <mailto:spoel at gromacs.org>
> > <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
> http://folding.bmc.uu.se
> > _______________________________________________
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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 <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> _______________________________________________
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> ------------------------------------------------------------------------
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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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