[AMBER] Cpptraj and hbonds

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Tue, 28 May 2013 16:06:26 +0200

  

Dear Amber users,

I'm trying to find some hydrogen bonds between
DNA and the spine water that it's found in minor groove. I have one
question about hbond command in cpptraj (version 13.1). I'm using
following line:

hbond solventhb ID out ${MOL}.hbonds :1-42.N3,O2
series solventdonor :WAT.O

In out file, I get this output format:

 1
0 31 7
97(12+31+),639(16+27+),1933(4+39+),5244(20+23+),7381(10+33+),10415(9+34+),10964(6+37+),


is this mean that oxygen atom 97 is forming two bonds with bases 12
and 31 (for example) in the same frame with the corresponding atoms, or
only a single one with the atom of 12 or 31? Is there any way to see if
is forming one or two bonds with the atoms of the base pair?

I know is
simply question, but I need to clarify this for my results.

Thank you
in advance.

Best regards,

Fernando

--
==============================================
 Fernando Martín
García 
 Molecular Modeling Group - Lab 312.1 
 Molecular Biology
Center "Severo Ochoa" 
 C/ Nicolás Cabrera, 1. 
 UAM University.
Cantoblanco, 28049 Madrid. Spain. 
 TEL: (+34) 91-196-4662 FAX: (+34)
91-196-4420
 Web:
http://fertoledo.wordpress.com/
==============================================
--
==============================================
 Fernando Martín
García 
 Molecular Modeling Group - Lab 312.1 
 Molecular Biology
Center "Severo Ochoa" 
 C/ Nicolás Cabrera, 1. 
 UAM University.
Cantoblanco, 28049 Madrid. Spain. 
 TEL: (+34) 91-196-4662 FAX: (+34)
91-196-4420
 Web:
http://fertoledo.wordpress.com/
==============================================
 
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue May 28 2013 - 07:30:02 PDT