[gmx-users] calculating properties of polyaromatics using gromacs

Fredrik Blomgren fredrik.blomgren at cit.chalmers.se
Tue Apr 10 15:56:15 CEST 2007

Dear All


I am a new user of Gromacs which means I am in the (somewhat painful)
process of learning how to use the program. My goal is to calculate
properties for polyaromatics containing nitrogen and sulfur. I want to use a
united atom force field and if I have understood it correctly I should be
able to use Gromos.


My problem is that I find it hard to get started. I am trying to test the
program for aniline (benzene with an amino group). I have a pdb-file of the
molecule and tried to run pdb2gmx which didn´t work because in my pdb-file I
didn´t specify a residue. This leads to my question: How does one run
pdb2gmx with a molecule that is not an amino acid residue or something else
that is stored in the database of Gromacs?


Best regards

Fredrik Blomgren


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