Olga Ivchenko wrote:
Dear All,

I just want to know if the programm PRODRG is able to generate for my ligand files with .top extension.


No, but it is trivial to interconvert .itp and .top manually:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

-Justin

I have two files one is itp format and other is gro using PRODRG.
If it is possible what is the name here :http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO

Yours sincerely,
Olga

2010/11/10 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>



    Olga Ivchenko wrote:

        Dear All,

        I have created creating topology file using  *prodrg_beta (using
        gromos 96 ff)
        <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta>*. When I
        am trying to run energy minimization it writes an error:


    Please consider carefully the caveats about PRODRG noted here
    (second paragraph):

    http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips


        Syntax error - File creatine.top, line 19
        Last line read:
        '[ moleculetype ]'
        Invalid order for directive moleculetype

        I looked at previoust mailing lists according this problem. I
        can not find direct answer.


    
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults

    Somehow you've cut and pasted such that you've got a [moleculetype]
    directive out of order.


        I tried to add this line in the topology file

        #include "ffG43a1.ff/DRGGMX.itp"

        An again an error:Fatal error:
        Topology include file "ffG43a1.ff/DRGGMX.itp" not found


    Then either the file doesn't exist or isn't within the search path
    grompp is trying.

    -Justin



        Please can you advice me on this.


        Yours sincerely,

        Olga





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

    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

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

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

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