[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:
> 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 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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