AMBER Archive (2003)

Subject: Has anyone ever used MEAD?

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Jan 20 2003 - 07:58:30 CST

Dear Ambers,
    I am trying to calculate the electrostatic potential onto a
protein-RNA complex using the MEAD suite. If somebody has ever used MEAD
I would appreciate a bit of help since the documentation is very scarce.
   So I have my .pqr file (created with ambpdb) and an .ogm file that
looks like this:
ON_GEOM_CENT 81 1.5
ON_GEOM_CENT 81 1.0
   I the MEAD distribution is written that if one uses -CoarseFieldOut
flag one does not need a .fpt file.
  But when I give the command:

potential -epsin 1.0 -CoarseFieldOut "file_name" MolName

  I receive the followin error message:

WARINING from potential main program:
Could not open field point file, comp_test.fpt, for reading. Exiting
without giving any potentials.
                   Centering Style grid dimension spacing
Coarsest level: ON_ORIGIN resolved to (0, 0, 0)) 81 1
Finest level: ON_ORIGIN resolved to (0, 0, 0)) 81 0.25

So, my question is why there is a need for an .fpt file since I used the
-CoarseFieldOut flag? Could also somebody explain what is a fpt file and
how can one obtain this file..is there a software which creates such
kind of files? And the second question is about the output: How does an
output from "potential" looks like? And how can one visualize the output
from MEAD suite?
I have to say that I studied the examples but neither one of them deals
with a "potential" calculation.
I would appreciate any kind of help.
Thanks a lot in advance,
Best wishes,
vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204