AMBER Archive (2003)

Subject: ptraj problem

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Fri Apr 04 2003 - 08:00:46 CST

When I am try to center a molecule to the center of the periodic box by using
the commands:

ptraj phenol_chcl3.top
trajin 6-5-1-md03.rst
center @1-13
trajout 6-5-1-md03.pdb pdb
go

the following messages come up

PTRAJ: Processing input file...
       Input is from standard input
trajin 6-5-1-md03.rst

PTRAJ: trajin 6-5-1-md03.rst
Checking coordinates: 6-5-1-md03.rst
center @1-13

PTRAJ: center @1-13
Mask [@1-13] represents 13 atoms
trajout 6-5-1-md03.pdb pdb

PTRAJ: trajout 6-5-1-md03.pdb pdb
go

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 1 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (6-5-1-md03.rst) is an AMBER restart file with box and velocity
information

OUTPUT COORDINATE FILE
  File (6-5-1-md03.pdb) is a PDB file

ACTIONS
  1> CENTER to box center via center of geometry, atom selection follows :1

Processing AMBER restart file 6-5-1-md03.rst

Set 1 .

PTRAJ: Successfully read in 1 sets and processed 1 sets.
       Dumping accumulated results (if any)

At the end it should tell me the atom selection, but it does not show any
atoms. Does that mean that it is not centering anything, because when I look
at the resulting pdb file nothing is changed and the MOL is still at the
boundary of the box and not at the center where I want it to be.

thanks for any help

Sophia Kondratova