AMBER Archive (2004)

Subject: AMBER: H Bonds

From: anshul_at_imtech.res.in
Date: Wed May 05 2004 - 15:07:01 CDT

dear amber users,
I am ttrying to analyse the H. bond pattern in various peptides. I am
using a right handed helix of a decapeptide. when i use carnal to find the
possible h bonds it gives a total of 13 H.Bonds. Insted of giving H bonds
between residue n and n+4 it also gives the same between residues n and
n+3. Is it normal or I am doing something wrong.

The other thing I want to ask is about the angle which is given in the
list file. The angle given by carnal is quite different from that given by
some other software. Can anyone through some light on this.

here are the input and the list file for my system.

FILES_IN
  PARM p1 ala10.prmtop;
  STREAM s1 ala10.inpcrd; FILES_OUT
  HBOND h1 hb_init LIST; DECLARE
  GROUP g1 (ATOM TYPE N);
  GROUP g2 (ATOM TYPE O); OUTPUT
  HBOND h1 DONOR g1 ACCEPTOR g2 STATS;
END

List

1 ( ALA 4 N )( ALA 1 O ) 3.335977 50.016235
1 ( ALA 5 N )( ALA 1 O ) 3.096780 18.832615
1 ( ALA 5 N )( ALA 2 O ) 3.336197 50.021879
1 ( ALA 6 N )( ALA 2 O ) 3.096576 18.820264
1 ( ALA 6 N )( ALA 3 O ) 3.335950 50.016080
1 ( ALA 7 N )( ALA 3 O ) 3.097679 18.839666
1 ( ALA 7 N )( ALA 4 O ) 3.336395 49.991904
1 ( ALA 8 N )( ALA 4 O ) 3.096568 18.858349
1 ( ALA 8 N )( ALA 5 O ) 3.336350 49.972242
1 ( ALA 9 N )( ALA 5 O ) 3.097235 18.838018
1 ( ALA 9 N )( ALA 6 O ) 3.336560 49.998391
1 ( ALA 10 N )( ALA6 O ) 3.096918 18.815361
1 ( ALA 10 N )( ALA 7 O ) 3.335742 50.034458

With regards,
Anshul

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