AMBER Archive (2008)

Subject: AMBER: watershell cero?

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Mon Jun 30 2008 - 11:22:11 CDT

Hello,
I am trying to do a ptraj analysis of "watershell" from a trajectory
obtained with NAMD/Amber.
Using this input file:

trajin ../trajectory.netcdf
watershell :1-168 watershell_out :WAT noimage
go

the calculation finished without errors, but wen I look to the generated
file "watershell_out" I can see that the first and second columns are cero
in all frames:

1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 0 0
14 0 0
15 0 0
16 0 0
(...)

Looking at the log file it seems that ptraj is considering well the solute
and solvent:

(...)

 Setting box to be an exact truncated octahedron, angle is 109.471221

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin ../trajectory.netcdf

PTRAJ: watershell :1-168 watershell_out :WAT noimage
Mask [:1-168] represents 2573 atoms
Mask [:WAT] represents 22788 atoms
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 10000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (../trajectory.netcdf) is a NetCDF AMBER trajectory with box info
with 10000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1> WATER SHELL: Output to watershell_out
      Imaging is disabled
      The first shell will contain water < 3.400 angstroms from
      the solute; the second shell < 5.000 angstroms...
      The solute atoms are :1-168
      The solvent atoms are :200-7795

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

(...)

Has anybody any idea of why the number of waters in both watershells are
cero???

Thank you very much in advance for your help,

Rebeca García Fandiño
Parc Cientific de Barcelona
rebeca_at_mmb.pcb.ub.es

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu