From chemistry-request@server.ccl.net Wed Jan 15 12:02:06 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0FH25V29129 for ; Wed, 15 Jan 2003 12:02:06 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18YqvW-0008CA-00 for chemistry@ccl.net; Wed, 15 Jan 2003 18:02:06 +0100 Message-ID: <3E259406.7050909@mpi-bpc.mpg.de> Date: Wed, 15 Jan 2003 18:01:58 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL Subject: MEAD help Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 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: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204