ASHWINI JAYAPRAKASH wrote:
Hi Mark,
Thank you for your valuable suggestion.I did go through the manual, but
I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file,
and if so I am not sure what the appropiate Type of angles, Type of
proper dihedrals, Type of improper dihedrals I have to enter.
If I choose the force field with option 0 then it gives me an error
saying residue AIB not found in residue topology.
I can't reconcile the above with your original problem. All you need to
do is have a coordinate file whose residue names correspond to those in
your .rtp file, and then atom names that correspond to those in the
residues in the .rtp file.
You should be careful to follow the advice in Step 2 of
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and if
appropriate http://wiki.gromacs.org/index.php/Parameterization
Mark
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