[gmx-users] how to write a rtp file for amido amine

lammps lammps lammp2forum at gmail.com
Sat Oct 9 10:27:27 CEST 2010

Hi everybody,

I want to use pdb2gmx command to create a .gro file and a .top file for
PAMAM whose repeat unit is amidoamine ( attached ).

---CH2--CH2--CO-NH-CH2-CH2-N    (see the attached figure)

The atom N have two same branches with --CH2--. I write the rtp file for it
as follows:

 [ atoms ]
   C1    opls_245    -0.050    1
 [ bonds ]
   C1    -N7
   C6    N7
   N7    +C1
   N7    +C1

It seems not work, which gives a wrong top structure. The question is how
can I deal with the two branches of N. Any suggestion is appreciated.

Thanks in advance.

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