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

[Justin A. Lemkul]

lammps lammps wrote:
> 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.
> 

http://www.gromacs.org/Documentation/File_Formats/specbond.dat

-Justin

> Thanks in advance.
> 
> 
> 
> 2010/10/9 Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>>
> 
> 
> 
>     ----- Original Message -----
>     From: lammps lammps <lammp2forum at gmail.com
>     <mailto: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
>     <mailto: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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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