Making IL water protein boxes

Powerpoint slides with directions to make IL/water/protein systems are below:

Kayla's 2/12/2015 group meeting presentation

The path on HYAK to the files accompanying the slides is below. Copy the entire directory into your own directory.

/gscratch/pfaendtner/vanouk/PRGmeeting0204

Also, you must have the following programs installed with links set in your .login file:

Antechamber, Tleap, Packmol, Acpype, and Gaussian

Rather than installing the above software, you can simply link to where others in the group have installed the programs. Below are the links in my .login file, which you can simply copy/paste into your own:

export GAUSS_SCRDIR=/gscratch/pfaendtner/YOUR_HYAK_USERNAME/gaussian
export g09root=/gscratch/pfaendtner/codes/G09
export AMBERHOME=/gscratch/pfaendtner/vjaeger/software/amber11b
export PATH=$PATH:/gscratch/pfaendtner/pburney/Software/packmol
export PATH=$PATH:/gscratch/pfaendtner/vjaeger/scripts/acpype
export PATH=$PATH:/gscratch/pfaendtner/vjaeger/software/amber11b/AmberTools/bin
. $g09root/g09/bsd/g09.profile

**Note that you must change YOUR_HYAK_USERNAME in the gaussian path, and make an empty directory called “gaussian” in your home gscratch directory.