AMBER: distance measurement in carnal and ptraj

From: <>
Date: Fri, 16 Apr 2004 15:56:33 -0500 (GMT)

Hi all the amber users,
I was trying to measure the distance between hydrogen bond acceptor and
donor in an alpha helical decapeptide using carnal, but the results i
got were far from reality. This distance (between the Nitrogen of first
residue and Oxygen of fifth residue) should be around 3.3 angstroms
but the one given by carnal in the output is around 9.6 angstroms. I would
like to know if the DIST option of carnal gives the distance which i am
looking for?
The input file used for the measurement is as follows:

  PARM P1 ala_an.prmtop;
  STREAM s1 ala_an.inpcrd;
  TABLE tab1;
  DIST dist1 N 2 O 6;
  DIST dist2 N 3 O 7;
  DIST dist3 N 4 O 8;
  DIST dist4 N 5 O 9;
  DIST dist5 N 6 O 10;
  DIST dist6 N 7 O 11;
  TABLE tab1 MEAS;


summary of the output :

Distance dist1: single 9.624
--Distance dist2: single 9.626
--Distance dist3: single 9.628
--Distance dist4: single 9.625
--Distance dist5: single 9.625
--Distance dist6: single 6.187

I also checked the same thing using ptraj but the results were almost the
same. Any kind of help in this direction will be of great help to me.

With regards

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Received on Fri Apr 16 2004 - 11:53:01 PDT
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