[gmx-users] (no subject)

SLN Prasad Reddy sreeyapu at rediffmail.com
Tue Jun 15 19:04:43 CEST 2004

An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040615/822fe99a/attachment.html>
-------------- next part --------------

    Hello gromacs users
          I am trying to run md-simulation on a protein having ATP. I could not run "pdb2gmx" with a protein having ATP. Then i was told by gromacs user to use prodrg. I followed a tutorial by name DRUG-Enzyme complex of Gromacs and i did as follows

  1.I submitted atp file alone to prodrg and if has given many out-put files from them i used DRGGMX.itp (renamed to atp.itp)  and DRGFIN.gro for futher use.

  2. I processed protein file alone with pdb2gmx
  3. Appended DRGFIN.gro at the end of protein.gro
  4. Then edited protein.top as follows
         - add  #include "atp.itp" after the force field parameter
         - Under [molecules] section : add ATP under compound and 
                                       2 under #mols.

     Then i processed with following commands

       - editconf
       - genbox
        I am successful with these two commands

      But when i used grommp command it is giving fallowing error
Fatal error: Invalid order for directive atoms, file ""atp.itp"",line 1

         Kindly suggest me a solution for this problem

        With many thanks in advance

         Prasad reddy

More information about the gromacs.org_gmx-users mailing list