Eudes Fileti wrote:
Hello Justin, thank you for answering!
I think I already have done what you suggested when I created my
ffbonded.itp and .rtp  files.

I am sending a piece of my topology and ffbonded.itp files.
Follows also the residue from .rtp and the configuration of glycol (.gro) so you can consider where I might be wrong and what I still must do.
Thanks again.


I appreciate the detail, but partial topologies are not useful for diagnosing anything. As I asked before, what is on line 40 of the topology? Which specific bond does this correspond to? What you need to determine is which bond type should be called and why it's not being found.

-Justin

eef

!!!  topol.top  !!!
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
Other               3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 HCP1 1 PA2 HOA 1 0.42 1.008 ; qtot 0.42 2 OC311 1 PA2 OHA 1 -0.65 15.9994 ; qtot -0.23 3 CC322 1 PA2 CA 1 0.05 12.011 ; qtot -0.18 4 HCA2 1 PA2 HA1 1 0.09 1.008 ; qtot -0.09
    ...
[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
1 2 1 2 3 1 3 4 1 ... [ pairs ]
;  ai    aj funct            c0            c1            c2            c3
1 4 1 1 5 1 1 6 1 ... [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 5 2 3 4 5 ... [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 9 ...
!!! ffbonded.itp !!!
[ bondtypes ]
; i      j     func        b0      kb
OC311   HCP1    1       0.0960   456056.0  ; par22 OH1 H
CC322   OC311   1       0.1420   334720.0  ; adm 11/08, glycerol
CC322   HCA2    1       0.1111   258571.2  ; par22 HA CT2
[ angletypes ]
; i       j       k    func       th0     cth      ub0       cub
HCP1 OC311 CC312 5 106.00 412.40 0.0 0.00 ; og 1/06 EtOH IR fit
[ dihedraltypes ]
; i     j       k       l       func    phi0    cp      mult
HCP1    OC311   CC322   HCA2    9         0.0   0.75    3  ; og methanol

!!! file.rtp !!!

[ PA2 ]
; Glycol
 [ atoms ]
   HOA    HCP1    0.420    1
   OHA   OC311   -0.650    1
    CA   CC322    0.050    1
   HA1    HCA2    0.090    1
   HA2    HCA2    0.090    1
    CB   CC322    0.050    2
   HB1    HCA2    0.090    2
   HB2    HCA2    0.090    2
   OHB   OC311   -0.650    2
   HOB    HCP1    0.420    2

 [ bonds ]
  OHA    HOA
  OHA    CA
   CA    HA1
   CA    HA2
   CB    CA
   CB    HB1
   CB    HB2
   OHB   CB
   HOB   OHB

!!! conf.gro !!!
GROningen MAchine for Chemical Simulation
   10
    1PA2    HOA    1  -0.248  -0.048   0.000
    1PA2    OHA    2  -0.177   0.017   0.000
    1PA2     CA    3  -0.052  -0.052   0.000
    1PA2    HA1    4  -0.041  -0.115   0.089
    1PA2    HA2    5  -0.041  -0.115  -0.089
    1PA2     CB    6   0.057   0.054   0.000
    1PA2    HB1    7   0.046   0.117  -0.089
    1PA2    HB2    8   0.046   0.117   0.089
    1PA2    OHB    9   0.182  -0.015   0.000
    1PA2    HOB   10   0.253   0.049   0.000
   3.00000   3.00000   3.00000


_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br


    ---------- Forwarded message ----------
    From: ** <gmx-users-requ...@gromacs.org
    <mailto:gmx-users-requ...@gromacs.org>>
    Date: Mon, Aug 23, 2010 at 7:00 AM
    Subject: gmx-users Digest, Vol 76, Issue 113
    To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>


    Send gmx-users mailing list submissions to
           gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>

    To subscribe or unsubscribe via the World Wide Web, visit
           http://lists.gromacs.org/mailman/listinfo/gmx-users
    or, via email, send a message with subject or body 'help' to
           gmx-users-requ...@gromacs.org
    <mailto:gmx-users-requ...@gromacs.org>

    You can reach the person managing the list at
           gmx-users-ow...@gromacs.org <mailto:gmx-users-ow...@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. Metallic boundary conditions (poj...@icp.uni-stuttgart.de
    <mailto:poj...@icp.uni-stuttgart.de>)
      2. Charmm to Gromacs: Polyols force field (Eudes Fileti)
      3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul)
      4. PMF (abdul wadood)
      5. Re: please, how edr data is xdr packed? (Sander Pronk)


    ----------------------------------------------------------------------

    Message: 1
    Date: Sun, 22 Aug 2010 17:52:46 +0200
    From: poj...@icp.uni-stuttgart.de <mailto:poj...@icp.uni-stuttgart.de>
    Subject: [gmx-users] Metallic boundary conditions
    To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
    Message-ID:
<3e5fe7757a687609503cad715e2a5d15.squir...@www.icp.uni-stuttgart.de
    <mailto:3e5fe7757a687609503cad715e2a5d15.squir...@www.icp.uni-stuttgart.de>>
    Content-Type: text/plain;charset=iso-8859-1


    Hi,

    thank you for your answer. What is then epsilon_r ?

    regards.



    ------------------------------

    Message: 2
    Date: Sun, 22 Aug 2010 14:42:43 -0300
    From: Eudes Fileti <fil...@ufabc.edu.br <mailto:fil...@ufabc.edu.br>>
    Subject: [gmx-users] Charmm to Gromacs: Polyols force field
    To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
    Message-ID:
           <aanlktikqtlshdgqsmprykc0x0fjiq+c_ydzcm6pke...@mail.gmail.com
    <mailto:aanlktikqtlshdgqsmprykc0x0fjiq%2bc_ydzcm6pke...@mail.gmail.com>>
    Content-Type: text/plain; charset="windows-1252"

    Olá pessoal,

    Recently, McKerrel published his CHARMM force field to polyols
    (JCTC, 2009,
    5, 1315).
    I am very interested in using it in GROMACS.

    For this, I began the transfer of the parameters with the following
    recipe:

    1) All atom types were added to the atomtypes.atp file;
    2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
    were added to the ffbonded.itp file;
    3) van der Waals and Coulomb parameters were inserted properly
    in ffnonbonded.itp;
    4) The residues were created in a new file named polyols.rtp.

    Well, pdb2gmx works fine! It generates the restraints file (posre.itp),
    configuration file
    (conf.gro) and topology file (topol.itp).  But when I run it in
    grommp, the
    default for
    parameters are not found. Something like:

    ERROR 6 [file topol.top, line 40]:
     No default Bond types

    I know I can insert the parameters by hand in each .top file
    generated by
    pdb2gmx.
    But what I need to do, so that grompp recognizes the default values
    automatically.

    Did I forgot some file? I'm making some mistake?

    Any suggestion is welcome!

    Muito obrigado!
    eef

    _______________________________________
    Eudes Eterno Fileti
    Centro de Ciências Naturais e Humanas
    Universidade Federal do ABC — CCNH
    Av. dos Estados, 5001
    Santo André - SP - Brasil
    CEP 09210-971
    +55.11.4996-0196
    http://fileti.ufabc.edu.br
    -------------- next part --------------
    An HTML attachment was scrubbed...
    URL:
    
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100822/8581cfd9/attachment-0001.html

    ------------------------------

    Message: 3
    Date: Sun, 22 Aug 2010 13:46:39 -0400
    From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
    Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
    To: Discussion list for GROMACS users <gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>>
    Message-ID: <4c71627f.1000...@vt.edu <mailto:4c71627f.1000...@vt.edu>>
    Content-Type: text/plain; charset=windows-1252; format=flowed



    Eudes Fileti wrote:
     > Olá pessoal,
     >
     > Recently, McKerrel published his CHARMM force field to polyols (JCTC,
     > 2009, 5, 1315).
     > I am very interested in using it in GROMACS.
     >
     > For this, I began the transfer of the parameters with the
    following recipe:
     >
     > 1) All atom types were added to the atomtypes.atp file;
     > 2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
     > were added to the ffbonded.itp file;
     > 3) van der Waals and Coulomb parameters were inserted properly
     > in ffnonbonded.itp;
     > 4) The residues were created in a new file named polyols.rtp.
     >
     > Well, pdb2gmx works fine! It generates the restraints file
    (posre.itp),
     > configuration file
     > (conf.gro) and topology file (topol.itp).  But when I run it in
    grommp,
     > the default for
     > parameters are not found. Something like:
     >
     > ERROR 6 [file topol.top, line 40]:
     >   No default Bond types
     >
     > I know I can insert the parameters by hand in each .top file
    generated
     > by pdb2gmx.
     > But what I need to do, so that grompp recognizes the default values
     > automatically.
     >
     > Did I forgot some file? I'm making some mistake?
     >

    Look on line 40 of the topology and see which atoms grompp is
    complaining about.
     You likely forgot to define the parameters for that particular bond
    type.

    -Justin

     > Any suggestion is welcome!
     >
     > Muito obrigado!
     > eef
     >
     > _______________________________________
     > Eudes Eterno Fileti
     > Centro de Ciências Naturais e Humanas
     > Universidade Federal do ABC — CCNH
     > Av. dos Estados, 5001
     > Santo André - SP - Brasil
     > CEP 09210-971
     > +55.11.4996-0196
     > http://fileti.ufabc.edu.br
     >

    --
    ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ========================================


    ------------------------------

    Message: 4
    Date: Mon, 23 Aug 2010 06:23:39 +0000
    From: abdul wadood <wadoodbiochem...@hotmail.com
    <mailto:wadoodbiochem...@hotmail.com>>
    Subject: [gmx-users] PMF
    To: gromacs <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
    Message-ID: <bay121-w7c84bc40d94bebf163356d0...@phx.gbl>
    Content-Type: text/plain; charset="iso-8859-1"


    Hi, All

    I am trying to calculate pmf for enzyme ligand complex using the
    tutorial of umbrella sampling.
    I have successfully created the unit cell around the protein and
    have solvated. The ions were also added by genion.
    But when I run the minimization step with the command
    grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
    the following error comes


    Fatal error:
    Molecule type 'NA+' contains no atoms


    I tried my best to solve the problem but could no succeeded.
    Any help to solve this problem will be highly appreciated.
    The topology file is attached.

    Thanks in advace

    Many regards

    Abdul Wadood,
    Research Scholar,
    Dr.Panjwani Center for Molecular Medicine and
    Drug Research,
    International Center for Chemical and
    Biological Science,
    University of Karachi, Karachi-75720, Pakistan.
    Email:wadoodbiochem...@hotmail.com
    <mailto:email%3awadoodbiochem...@hotmail.com>



    -------------- next part --------------
    An HTML attachment was scrubbed...
    URL:
    
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/6c9f9ed2/attachment-0001.html

    ------------------------------

    Message: 5
    Date: Mon, 23 Aug 2010 09:56:26 +0200
    From: Sander Pronk <pr...@cbr.su.se <mailto:pr...@cbr.su.se>>
    Subject: Re: [gmx-users] please, how edr data is xdr packed?
    To: Discussion list for GROMACS users <gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>>
    Message-ID: <31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se
    <mailto:31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se>>
    Content-Type: text/plain; charset="us-ascii"

    As David said, the reading/writing is done in src/gmxlib/enxio.c,
    but you could also read edr files indirectly through gmxdump: that
    should also give you an idea of the type of information in those files.



    On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:

     > Hi there,
     >
     > I am trying to use python xdrlib module to read edr files but not
    knowing how the data is packed using the xdr protocol makes my work
    very difficult, if not impossible.
     >
     > Would someone kindly tell me how data is packed in the edr file?
    Or where it is the gromacs code so I can try to figure out a way?
     >
     > I've read http://tools.ietf.org/html/rfc1832.html and for
    reference, see topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".
     >
     > My other option would be using a parsing code to read g_energy
    output but this seems very silly.
     >
     > Many thanks in advance,
     >
     > Alan
     >
     > --
     > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
     > Department of Biochemistry, University of Cambridge.
     > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
     > >>http://www.bio.cam.ac.uk/~awd28<<
     > --
     > gmx-users mailing list    gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>
     > http://lists.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-requ...@gromacs.org
    <mailto:gmx-users-requ...@gromacs.org>.
     > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

    -------------- next part --------------
    An HTML attachment was scrubbed...
    URL:
    
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/4a7ed781/attachment-0001.html

    ------------------------------

    --
    gmx-users mailing list
    gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at http://www.gromacs.org/search before
    posting!

    End of gmx-users Digest, Vol 76, Issue 113
    ******************************************



--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to