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
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