AMBER Archive (2004)

Subject: AMBER: Preparing complex in Xleap for Amber calculations

From: warka_at_il.waw.pl
Date: Wed Mar 17 2004 - 10:02:38 CST

When I prepare the complex of protein with ligand the program Xleap add
automatically the N and C terminal, and when I save topology and
coordinate files the program writes me such command:

Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CVAL 1
        NMET 1

I don't know if it can cause any problems during calculations in Amber,
because in topology file there are some strange words BLA in the start and
the end point of the receptor, as you can see below:

%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA M
E M E 3 E E B E E M E M E M E 3 E 3 E E
E 3 E E 3 E E E M E M E M E 3 E E 3 E 3
E E E 3 E E E M E M E M E 3 E E S E [...]
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA M M 3 E E 3 E E 3 E E S E M M
E E M E E M E E M E E M 3 E E B E E E M
E 3 E E E M E E M M B E B E S B E B E S
E M M M E

I also have some problems with understanding the "tail" and "head" in Xleap

Head atom: null
Tail atom: .R<AM5 472>.A<C21 59>

because the tail atom is here the atom of the ligand in complex ( protein
-ligand).
Is it correct?

Malgorzata Jaronczyk

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