[gmx-users] How to obtain the .gro and .top files for dendrimers

[Mark Abraham]

wuxiao wrote:
> Dear gmx users,
>   On current, I plan to study a dendrimer (like PAMAM) using MD 
> simulations available in GROMACS. As is well-known, the .gro and .top 
> files are the start points for running MD simulations in GROMACS. 
> However, the question how to obtain the files for dendrimers puzzles me 
> too much, since the dendrimers have a complex dendritic structure. The 
> mail-list and the manual seem not give helpful clues on doing it. Are 
> there someone that have the experiences to do so? Could you share these 
> experiences with us? Any suggesstion would be acknowledged greatly.

Unfortunately the main topology builder for GROMACS (pdb2gmx) is fairly
specific for head-to-tail polymers like protein and DNA. If you have an
existing generator for coordinates in some suitable format (PDB, .gro,
etc.), then you can probably make pdb2gmx work with careful use of
specbond.dat and appropriate .rtp file entries. You will probably need
to make versions of your "residues" that are terminated, since the
pdb2gmx termination methods won't cope with more than two termini. A
detailed knowledge of much of chapter 5 of the manual will be required.

There is no existing GROMACS tool for generating coordinate files, so
you are on your own here.

Mark