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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