AMBER Archive (2004)

Subject: RE: AMBER: paramitrization problem

From: lei jia (jial_at_broyde.nyu.edu)
Date: Tue Jun 08 2004 - 10:00:11 CDT

Dear Ross,

Thank you for your suggestions. I think leap has loaded the parm file
since the lines at initiation are like these:

Welcome to LEaP!
Sourcing leaprc: ./leaprc
Log file: ./leap.log
Loading parameters: ./parm99.dat
Loading library: /usr/local/etc/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/etc/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/etc/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/etc/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/etc/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/etc/amber7/dat/leap/lib/solvents.lib
>

It sourced the leaprc file, which was modfied by adding new atom types,
located in the current folder. I also found there is a leaprc.ff99 file
in the amber folder. I didn't add new atom types to the leaprc.ff99
file. If I source the leaprc file instead of the leaprc.ff99 file, will
the leaprc.ff99 be read when I save the topology file? There are no
parameters missing when I checked unit. And I have no problem to add
ions. But I can't add water right and save the topology file.

Thanks,

Lei Jia

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