Subject: MEAD help

From: Vlad Cojocaru <[email-masked]>
Date: Wed, 15 Jan 2003 18:01:58 +0100

Dear CCLers,
   I am trying to use MEAD for the first time. Since the documentation 
is very scarce I would like to ask  somebody that has already calculated 
electrostatic potentials on macromocules using "potential" from MEAD 
suite to give me some hints.
   I am refering here to a simple basic calculation. I tried to look at 
the examples in the distribution but there is no examples for how to 
take a structure from the pdb and calculate the potential and 
visualizing it. All the examples deal with more advanced stuff.
   I tried "potential -epsin 1.0 -CoarseFieldOut file molname" on a pqr 
file created with ambpdb (AMBER) and a ogm file  that looks like below
ON_GEOM_CENT 41 1.0
ON_GEOM_CENT 41 0.25
   I got some warnings and errors that look like this:

WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice,
WARNING: SAVanal_calc: vertex found with count = 2
WARNING: SAVanal_calc: vertex found with count = 2
WARNING: SAVanal_calc: vertex found with count = 1
WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the 
lattice,
WARINING from potential main program:
Could not open field point file, comp_test.fpt, for reading.  Exiting 
without giving any potentials.

   Woould I ask too much if I ask somebody to shortly explain these? 
About the last one in the README file it is said that an .fpt file is 
not mandatory with the option "-CoarseFieldOut file" so I used the flag 
but still it gave me the error. If this file .fpt is mandatory could 
somebody tell me what is the ".fpt" file and can I get a file like this 
for a molecule....it is not explain in the README file from MEAD 
distribution

Thanks a lot in advance for any help. Hope I did not ask too much
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: [email-masked]
home tel: ++49-551-9963204