Jagannath Mondal wrote:
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 ?
if you have .top you don't need to run pdb2gmx
you can use pdb file as input to grompp
2. I have one more query. What is the use of 'define' string in
toplgy files?
chapter 5 in the manual
Thanks.
Jagannath MOndal
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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