AMBER Archive (2001)

Subject: xleap silly thing

From: Jose Ramon Blas (jramon_at_sgbq.bq.ub.es)
Date: Wed Jan 31 2001 - 14:32:20 CST

For xleap users,

I want to create a topology file for a free energy calculation.
But it is my first time doing so by using XLEAP.
What have I done?

I have the 2 residues defined in a library. One of them is an ion.

> loadoff myfile.lib
> edit mymolecule (contains the 2 residues)
... Here I modify the PERT columns, I hope that properly .....
(The modification consists only in changing the ATOM TYPE & NAME of the ion,
charge remains the same. The parameters for the new atom type previously
loaded. They are different. I have checked it.)

> check mymolecule (everything found)
> saveamberparmpert mymolecule jjjj.top jjjj.crd

I have followed the same path changing and maintaining the atom type.
Surprise!!
The topology file created in both cases is the same (the parameters, not the
atom names/types, which is the only changed thing).

Sure, I have missed a step. But, after reading the manual, I do not find where.

I will be very glad with your suggestions,

Blas