Jamie Seyed wrote:
Hi Justin,
Oh yes. I had a line that include ff again and I deleted that (is that ok)? now I got a new error related to "number of coordinates in

That's more than OK, that's correct. As Mark pointed out, there should only ever be one invocation of [ defaults ] in a topology.

coordinate file does not match topology..." I should fix this one now!!

Simple one to fix. Figure out where the duplicate or missing molecules are within the topology. I'm guessing your molecule.itp was really a molecule.top, complete with [ defaults ], [ system ], and [ molecules ] directive, right? None of these should be present in an .itp file, only a .top.

-Justin

Thanks a lot/Jamie

On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:


    Can you post the contents of molecule.itp?  The first #include for
    the force field is likely not the problem; you've probably #included
    it again in molecule.itp.

    -Justin

    Jamie Seyed wrote:

        Dear all,
        I have a topology contains line as below. I do not understand
        what is wrong with it that I get an error
        -----------
         Program grompp, Version 4.0.5
         Source Code file: topio.c, line: 415
         Fatal error:
         Syntax error-File ffoplsaa.itp, line 18
         last line read:
         '[defaults]'
         Invalid order for directive defaults
        --------------
        according to the page
        
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
        I do not have twice default section... SO I do not know exactly
        which files I should check... It says topology and ff. Topology
        that I am using in grompp is as below and the ffoplsaa.itp has
        only one default section...
        Would you please help me to solve the problem.
        topol.top: -------------
        #include "ffoplsaa.itp"
        #include "spce.itp"
        #include "molecule.itp"
        [system]
        fullerene in water
        [molecules]
        molecule   1
        SOL       1000
        --------------------
        Many Thanks in Advance and I appreciate your help/Jamie

         On Mon, Aug 10, 2009 at 5:46 PM, Jamie Seyed
        <jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>
        <mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>>>
        wrote:

           Dear Vitaly,
           topol.top: -------------
           #include "ffoplsaa.itp"
           #include "spce.itp"
           #include "c80ch3.itp"
           [system]
           fullerene in water
           [molecules]
           C80CH3   1
           SOL       1000
           --------------------
           my command is:
           grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr  -maxwarn 10
               Thank you for helping me out to solve the problem/
        Regards/Jamie
                   On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban
           <vvcha...@gmail.com <mailto:vvcha...@gmail.com>
        <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>> wrote:

               Jamie,

               The idea is the same. Some directive is not at its place. I
               cannot say
               which is exactly because I don't see all the picture with
        your
               topology file (+included files). Write the sequence of
        directives as
               they go in .top (+included .itp) and then we will see
        what sections
               must be shifted or maybe just swapped.

               Vitaly

               On Tue, Aug 11, 2009 at 12:34 AM, Jamie
               Seyed<jamie.se...@gmail.com
        <mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com
        <mailto:jamie.se...@gmail.com>>> wrote:
                > Hi Vitaly,
                > When I add it back, I got the old error
                > -----------
                > Program grompp, Version 4.0.5
                > Source Code file: topio.c, line: 415
                > Fatal error:
                > Syntax error-File ffoplsaa.itp, line 18
                > last line read:
                > '[defaults]'
                > Invalid order for directive defaults
                > -----------
                > Now do you have any idea??? I appreciate your help/Jamie
                >
                > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed
               <jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>
        <mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>>>
        wrote:
                >>
                >> Hi Vitaly,
                >> I did it because I read from
                >>
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
                >> that says:
                >> "One solution is to simply comment out (or delete)
        the lines
               of code out
                >> in the file where it is included for the second time
        i.e.,
               ..". So if it is
                >> the case I am going to undo it to see what happens...
        I will
               let you know.
                >> Thanks/Jamie
                >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban
               <vvcha...@gmail.com <mailto:vvcha...@gmail.com>
        <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>>>

                >> wrote:
                >>>
                >>> Why did you comment out [defaults] in ffoplsaa.itp? The
               general idea
                >>> is that the sections in the resulting topology file
        (after
               including
                >>> #include's) must be placed in the strict order.




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

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    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

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

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

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