From: Qing Zhang <>
Date: Sat 3 Aug 2002 18:12:24 -0700 (PDT)

--- Cozmuta <> wrote:
> Hi,
> Seems that something went wrong during the
> installation of amber so I did
> not have at all the PROTON_INFO file. I reinstalled
> amber and now I am
> able to find the file in $AMBERHOME/dat/. However
> when I try to protonate
> my structure I get the following error message:
> 345 % protonate_shell
> 6998 atoms read from file
> This version only dimensioned for 7000 atoms!
> Is it possible to change the dimension somewhere in
> the program?

In $AMBERHOME/src/protonate/protonate.h, you can see:

      parameter (MAXAT=7000)

Change the value of MAXAT to some number larger than
the amount of atoms in your system. Save the file,
then type "make" to compile a new protonate executable
file, or type "make install" to also install the new
protonate into $AMBERHOME/exe.

Good luck,

Qing Zhang

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Received on Sat Aug 03 2002 - 18:12:24 PDT
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