[gmx-users] Rtp for polymer.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 5 07:06:04 CET 2009

varsha gautham wrote:
> Hello  justin,
> Am sorry to say that its not useful.But what i mean is that the rtp 
> constructed manually is building up the polymer and generating topology 
> files and gro files.
> But when i look into the gro file with vmd the connectivity between each 
> of the monomer is not built.

VMD merely guesses the connectivity - there's none specified in a .gro 
file, which is purely a set of coordinates. A .top file defines a 
topology. If your input structure doesn't conform to VMD's heuristics, 
then it won't show a bond.

You can't judge the success of your .rtp construct without looking at 
the *topology* pdb2gmx produced.

> That is my polymer consists of 10 monomer 
> units with ben and primary amine unit as a block polymer.
> How can i include the connectivity information between these two in a 
> rtp file?I can include that in session called bonds. But how to do 
> that??And i want some help
> regarding the workflow that is how gromacs interpreting each of the rtp, 
> atp ,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are 
> there any materials available other than manual..If so please let me know

Try http://wiki.gromacs.org/index.php/.top_file and links thereon.


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