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

[Mark Abraham]

----- Original Message -----
From: lammps lammps <lammp2forum at gmail.com>
Date: Saturday, October 9, 2010 19:27
Subject: [gmx-users] how to write a rtp file for amido amine
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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. 

pdb2gmx is intended only for work with linear heteropolymers. Any more complex things (e.g. disulfides, branched structures) have to be engineered using the specbonds.dat mechanism.

Mark

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