AMBER: About Hbond calculations using ptraj

From: javier perez <xavip.qorws1.uab.es>
Date: Mon, 28 Jun 2004 19:43:37 +0200

Hi Amber community,

I want to calculate hydrogen bondings (angles, distances, %occupied) using
ptraj. I create a trajin file where I define a list of hydrogen bond
"donors" and hydrogen bond "acceptors".
Then, type the option hbond:
 
hbond distance 3.5 solventneighbor 6 solventdonor WAT O solventacceptor WAT O
H1 solventacceptor WAT O H2

I run the calculation and finally, I obtain a result where there are
information about "donors", "acceptors", "acceptorsH", angles, distances and
%occupied.

In this calculation, intra-residue interactions are not included. I read that
information when I go to the HBOND SUMMARY:

HBOND SUMMARY:

      data was sorted, intra-residue interactions are NOT included,
      Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information dumped for occupancies > 0.00

I would like to take into account all the intra-residue interactions. How can
I include these interactions??

Thanks in advance,


Xavi Perez

Chemoinformatic
Department of Chemistry
Universitat Autonoma de Barcelona
Bellaterra, Spain



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Received on Wed Jun 30 2004 - 11:53:00 PDT
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