AMBER Archive (2005)

Subject: AMBER: Radial Distribution functions by ptraj

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Thu Dec 01 2005 - 13:44:02 CST

Dear Amber users,

I am trying to calculate rdf function by using ptraj. Here is my input file:

trajin md1.mdcrd.gz
trajin md2.mdcrd.gz
trajin md3.mdcrd.gz
trajin md4.mdcrd.gz
trajin md5.mdcrd.gz
radial rdf 0.1 10.0 :WAT :1-94
go

It reads the files alright. However, after processing trajin md2.mdcrd.gz
it gives segmentation fault !

I have gone through the amber archive carefully and have noticed that some
other users also have mentioned this. However, I could not find out why it
is happening. Am I wrong while mentioning the solute and solvent mask?
Ptraj with my input gives following:

ACTIONS
  1> RADIAL DISTRIBUTION FUNCTION: Output to rdf_mon1
      spacing is 0.100
      maximum is 10.000
      [This implies 99 bins]
      density is 0.033
      RDF will bin all solute-mask to solvent-mask distances
      Solvent atom selection is :95-4589
      Solute atom selection is :1-94

My system has 94 amino acids and 95 to 4589 are water molecules. Does
'radial rdf 0.1 10.0 :WAT :1-94' mean that RDF by ptraj will represent the
interactions of all the atoms in 94 residues (~1500) with all the water
molecules (~4500) ? What will be my input if I want to calculate RDF for a
single atom or a single residue?

Any help will be of great help to me.

Thanks,
-Priti.

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