[gmx-users] CSDs
jahanshah ashkani
ashkani_2003 at yahoo.com
Tue Nov 6 21:34:56 CET 2007
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
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
>
>
> ----- 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: 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> wrote:
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> >> 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)
> >>
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> >>
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----------------------------------------------------------------------
> >> Message: 1
> >> Date: Thu, 1 Nov 2007 16:17:32 +0100
> >> From: "Qiao Baofu" <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>
> >> Message-ID:
> >>
> >>
> > <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 --------------
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> >> ------------------------------
> >>
> >> 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>>
> >> 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>>
> >> Message-ID: <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>
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at
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<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>
> 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>>
> >> 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>>
> >> Message-ID:
> >>
> >>
> > <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>>:
> >>> 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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> > 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>
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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