[gmx-users] Query regarding PDB2gmx

[Jagannath Mondal]

HI,
     I am a gromacs beginner. I am trying to simulate a non natural  
peptide. I have prepared a standalone  molecule .itp file for my  
molecule  and I have prepared a corresponding topology file 
(topol.top) which include the .itp file.

      First, I was trying to get a .gro file from the PDB file of my  
molecule. But, when-ever I try to use the pdb2gmx command it always  
ask to choose among    the shared topologies present in gromacs  
library in stead of refering to my own topology file present in  
working directory. And it also over-writes my own topology file. My  
question is :
      1. How can I prepare    a   .gro file using  my  own topogy  
file from my PDB file  i.e How I can force the gromacs to look into  
my present directory in stead of looking into the shared gromacs  
topologies  ?

    2.  I have one more query. What is the use of 'define' string in  
toplgy files?
    Thanks.
  Jagannath MOndal