[gmx-users] rtp entry

ASHWINI JAYAPRAKASH ashjay012 at yahoo.com
Fri Jun 22 02:13:08 CEST 2007

Hi Mark,
  I have changed the atom name in the co-ordinate file. Now I get an error saying : 
  Residue "pop" not found in residue database
  My co-ordinate file consists of protein, popc  and sol. Do I have to add the itp files of popc and sol to the rtp file.

Mark Abraham <Mark.Abraham at anu.edu.au> 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

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