AMBER Archive (2006)

Subject: RE: AMBER: RDF output

From: Jardas sucuriba (jarda_s_at_hotmail.com)
Date: Wed Aug 30 2006 - 16:31:08 CDT

Hi again

I saw in the amber list that someone had the same problem as me
(http://amber.ch.ic.ac.uk/archive/200507/0374.html) but the message had no
answer...Pehaps my questions are too basic but I really donīt understand why
the rdf values that come in the second column of the volume.xmgr file are
all zero but not in the standard.xmgr file. I am worry with this because I
donīt know if the rdf values that come in the standard.xmgr are correct...Is
there something wrong with my input file? Please help me.

Thanks
Jardas

>From: "Jardas sucuriba" <jarda_s_at_hotmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: AMBER: RDF output
>Date: Tue, 29 Aug 2006 14:48:29 +0000
>
>Hi
>
>I have tried to calculate the radial distribution functions for specific
>residues with water and I have some questions related with the output:
>
>1) The amber 8 manual says that three files are produced, but I didnīt
>obtain the file corresponding to the carnal style RDF. Does anyone know
>why?
>
>2) The rdf values that come in the second column of the volume.xmgr file
>are all zero but the standard.xmgr file contains the "normal/expected"
>values. Is this correct? What the difference in the values that should I
>obtain?
>
>
>My input file is:
>
>trajin md2_1.mdcrd.gz
>trajin md2_2.mdcrd.gz
>center origin :1-256
>image origin center familiar
>radial C8rdf_O.05_8.xmgr 0.05 8.0 :WAT_at_O :256_at_C8
>radial N11rdf_O.05_8.xmgr 0.05 8.0 :WAT_at_O :256_at_N11
>
>
>Thanks
>Jardas
>
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