AMBER Archive (2008)

Subject: AMBER: Prepgen

From: Rajendra P. OJHA (
Date: Wed May 14 2008 - 04:45:47 CDT

Dear Professor Ross Walker,
      We are not able to create the parameter for new
molecules. As mentioned in the program some additional
atoms were added at both ends to calculate the
potential from G03. But, when machine.dat file was
used to calculate the charges at the atomic centers.
It gives the same charges which were in the original
molecule. As a result of which the total charge on the
molecular system is not zero, which was mentioned in
the machine.dat file.
      I send it on AMBER net but we have not yet
received any reply.
      Please rectify the problem and suggest what to
     Thank you very much and with regards,

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