[gmx-users] rtp entry

[ASHWINI JAYAPRAKASH]

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.
   
  Thanks,
  Aj

Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
  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
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


 
---------------------------------
We won't tell. Get more on shows you hate to love
(and love to hate): Yahoo! TV's Guilty Pleasures list.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070621/cf9fa254/attachment.html>