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

[lammps lammps]

Hi  Mark,

Thanks for your reply. But, I do not know the meaning of the columns in
specbonds.dat. I also  do not find any information in the manual 4.0.

Could you provide something about the specbonds.dat or give some
explanations.

Thanks in advance.



2010/10/9 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> ----- 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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-- 
wende
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