AMBER Archive (2004)

Subject: Re: AMBER: Preparing complex in Xleap for Amber calculations

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 17 2004 - 10:39:27 CST

On Wed, Mar 17, 2004, warka_at_il.waw.pl wrote:
>
> 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

Above is normal.

>
> 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

Above is also normal.

>
> 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?
>

You probably don't need to work about this. "head" and "tail" are only
used to join residues of a polymer together. Just be sure in your initial
pdb file to have a TER card between the protein and the ligand, so that leap
knows to create them as separate molecules.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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