[gmx-users] Query regarding PDB2gmx
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 8 08:48:13 CEST 2007
Jagannath Mondal wrote:
> 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
> Jagannath MOndal
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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