AMBER Archive (2003)

Subject: Probelm with the generation of topology file

From: Jash, Panchatapa (panchatapa.jash_at_marquette.edu)
Date: Tue Jan 21 2003 - 12:01:45 CST

Hi Everybody,
I'm trying to run the MD simulation 20A long cylinder made of dummy atoms surrounded by another type of dummy atoms (i.e., with different force field parameters) and filled with water. But I've some problem during the preparation of the topology file using xleap. With the amberparm option the topology and the coordinate files are made but in the pdb file (ambpdb option has made it) shows that some water molecules are considered as a residue and in some cases each H and O are recognized as a residue; sometimes each dummy atom is appearing as a single residue, sometimes a collection of atoms are considered as a residue; this is unlike the initial pdb file (where each dummy atom was a residue and I wanted the each water molecule to be considered as a residue) which I've loaded before going to start the work. it's obvious, from the topology generated pdb file, that something is wrong with the topology file generated by xleap but I don't understand how to manage this problem as d!
on't know what is wrong exactly.
 
Thanks so much for any advice. Could you please send the reply to Email as I'm not subscribed to the list right now.
 
panchatapa