[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:
>  >
>  >> Send gmx-users mailing list submissions to
>  >>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>  >>
>  >> 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
>  >>     gmx-users-request at gromacs.org
 <mailto:gmx-users-request at gromacs.org>
>  >>
>  >> You can reach the person managing the list at
>  >>     gmx-users-owner at gromacs.org
 <mailto:gmx-users-owner at gromacs.org>
>  >>
>  >> 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" <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 --------------
>  >> 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>>
>  >> 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
>  >> 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>.
>  >>> 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 ===
>  >
>  >
>  > __________________________________________________
>  > Do You Yahoo!?
>  > Tired of spam?  Yahoo! Mail has the best spam protection around
>  > http://mail.yahoo.com
>  >
>  > _______________________________________________
>  > 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 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>.
>  > 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
> _______________________________________________
> 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 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>.
> 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    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.
> 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    spoel at gromacs.org   http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list    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.
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 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071106/d4585657/attachment.html>


More information about the gromacs.org_gmx-users mailing list