Dear N. Nandi,
The 5'-terminal fragment has to bear a 5'-HO hydroxyl group in the
Amber force field topology database.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
If you want a 5'-POX... group you will have to generate a new
molecular fragment. For generating a new molecular fragment you might
be interested in the R.E.D. tools and/or in R.E.D. Server.
More generally, to get help you should better describe what you want
to do, and what are the error messages you get...
regards, Francois
> We are trying to load the tRNA molecule for simulation in AMBER. But
> 5'terminal phosphate group cannot be loaded. Then we tried to
> generate the parameter file for the group using antechamber but we
> faced the same problem. The following line was appeared on the
> terminal:
> 4atoms not in the residue templates
> andthe atoms are
> OP1
> P
> OP2
> OP3
> would someone please help us to get the way? We will be thankful to
> know the solution.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 06 2013 - 06:00:03 PDT
