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.
Mark
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