AMBER Archive (2005)

Subject: AMBER: radial distribution function

From: Myunggi Yi (myunggi_at_csit.fsu.edu)
Date: Mon May 09 2005 - 13:36:43 CDT

Dear Amber users,

I have run constant pressue and temp simulation with truncated
octahedron water box.(Amber8)
Now I'm trying to calculate rdf function by using ptraj, but I've got an
error message.

This is my input file.
=======================
trajin md1.mdcrd.gz
trajin md2.mdcrd.gz
trajin md3.mdcrd.gz
trajin md4.mdcrd.gz
radial fala 0.1 10.0 :WAT_at_O @CB
go
=======================

,And the following is the output on screen.

=======================
...............................
...................................
Scanning Box
Read in box information...
Successfully completed readParm.

Initializing state: detected PBC beta angle in prmtop that is not 90.0!
Assuming this box is a truncated octahedron, angle is 109.471221

PTRAJ: Processing input file...
        Input is from file rdf.ptraj

PTRAJ: trajin md1.mdcrd.gz
Checking coordinates: md1.mdcrd.gz

PTRAJ: trajin md2.mdcrd.gz
Checking coordinates: md2.mdcrd.gz

PTRAJ: trajin md3.mdcrd.gz
Checking coordinates: md3.mdcrd.gz

PTRAJ: trajin md4.mdcrd.gz
Checking coordinates: md4.mdcrd.gz

PTRAJ: radial pure-fala 0.1 10.0 :WAT_at_O @CB
Mask [:WAT_at_O] represents 1776 atoms
Mask [@CB] represents 4 atoms
FYI: No output trajectory specified (trajout), none will be saved.

PTRAJ: Successfully read the input file.
        Coordinate processing will occur on 20000 frames.
        Summary of I/O and actions follows:

INPUT COORDINATE FILES
   File (md1.mdcrd.gz) is an AMBER trajectory (with box info) with 5000 sets
   File (md2.mdcrd.gz) is an AMBER trajectory (with box info) with 5000 sets
   File (md3.mdcrd.gz) is an AMBER trajectory (with box info) with 5000 sets
   File (md4.mdcrd.gz) is an AMBER trajectory (with box info) with 5000 sets

OUTPUT COORDINATE FILE
   NULL entry

ACTIONS
   1> RADIAL DISTRIBUTION FUNCTION: Output to pure-fala
       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 :13-1788_at_O
       Solute atom selection is :2_at_CB,:5_at_CB,:8_at_CB,:11_at_CB

Processing AMBER trajectory file md1.mdcrd.gz

Set 1 .................................................
Set 50 .................................................

Set 4900 .................................................
Set 4950 .................................................
Set 5000 Segmentation fault (core dumped)
======================

Is there anyone who knows what the problem is? 

-- 
Best wishes,

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