AMBER Archive (2002)

Subject: Re: PROTON_INFO

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Sat Aug 03 2002 - 20:12:24 CDT

--- Cozmuta <ioana_at_wag.caltech.edu> 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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