AMBER Archive (2002)

Subject: PTRAJ: radial distribution function

From: A. Hungie (hungie01_at_hotmail.com)
Date: Wed Jul 17 2002 - 10:58:14 CDT

Dear All,

I calculated RDF of WAT solvating DNA (16 residues) using ptraj.in
==>
trajin md.traj 1 100 1
radial rdf_DNA-WAT 0.05 8.0 :WAT :1-16
go
<==

I obtained output without any problem.

Then I tried to calculate RDF of Na+ solvating DNA using input
==>
trajin md.traj 1 100 1
radial rdf_DNA-Na+ 0.05 8.0 :Na+ :1-16
go
<==

when the running reached the last snapshot, there was error message as
below;
------
.
.
.
PTRAJ: radial rdf_DNA-Na+ 0.05 8.0 :Na+ :1-16
Mask [:Na+] represents 14 atoms
Mask [:1-16] represents 504 atoms
FYI: No output trajectory specified (trajout), none will be saved.
.
.
.
ACTIONS
  1> RADIAL DISTRIBUTION FUNCTION: Output to rdf_DNA-Na+
      spacing is 0.050
      maximum is 8.000
      [This implies 159 bins]
      density is 0.033
      RDF will bin all solute-mask to solvent-mask distances
      Solvent atom selection is :17-30
      Solute atom selection is :1-16

Processing AMBER trajectory file md.traj

Set 1 .................................................
Set 50 .................................................
Set 100 Segmentation fault

*****

Could you please point me to overcome this problem?

Thank you very much in advance.

Regards,
Hungie

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