タンパク関連のDB
ターゲットタンパク研究プログラム TPリンク集 - データベース編 -
http://www.tanpaku.org/tp_links/databases.php
Supertarget: an extensive web resource for analyzing 332828 drug-target interactions.
http://bioinf-apache.charite.de/supertarget_v2/index.php
TargetMine
http://targetmine.nibio.go.jp/targetmine/begin.do
Therapeutic target database
http://bidd.nus.edu.sg/group/TTD/TTD.asp
bolzmann ratio
bc 定義式
define r(x) { return e(-x/(0.0083144621*298.5)); }
r(1)
.66836390382968971570
r(2)
.44671030794246272302
r(5)
.13337208332565118291
r(10)
.01778811261062444230
r(-0)
1.00000000000000000000
r(-1)
1.49619091376726517516
r(-2)
2.23858725043972393549
r(-5)
7.49782094621950036996
r(-10)
56.21731894156788385925
mac tips/ まっく
- .bashrcのロード。
~/.bash_profileに以下を記述。
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi
- dsclコマンド（v10.5以降）
directory service command line。ユーザ管理に利用。
$ dscl . -list /
$ dscl . -read /Users/egghead
$ dscl . -read /Users/egghead UserShell
$ dscl . -search /Users UniqueID 501
- install_name_tool コマンド
共有ライブラリパスの変更
$ otool -L executable
$ install_name_tool -change not_found.dylib existing.dylib executable
- roモードでmount_ntfs コマンド
Check the "Device Node:" & "Mount Point:" by the following command.
$ diskutil info "/Volumes/drive name"
Unmount drive. and execute mount_ntfs with "-o rw" option
$sudo mount_ntfs -o rw /dev/disk?s? "/Volumes/drive name"
qchem tips
#001 実行方法
$ source /usr/local/qchem-4.0.1/qcenv.sh
$ qchem --help
You are running Q-Chem version: 4.0.1
Error: input file --help does not exist !
/usr/local/qchem-4.0.1/bin/qchem [-save] [-par|-seq] [-nt nthreads] [-np nprocs] input output scratchDir
#002 入力ファイルの例
一点計算(dft_b3lyp_h2o.in)
$comment0
Sample test of the B3LYP hybrid functional.
$end$comment
water B3LYP/6-31G* Single point energy
$end$molecule
0 1
O
H1 O OH
H2 O OH H1 HOHOH = 0.947
HOH = 105.5
$end$rem
EXCHANGE B3LYP
CORRELATION None Hybrid functional, correlation incorporated
BASIS 6-31G* Basis Set
IPRINT 3
NBO true Do NBO analysis
$end
構造最適化の後、振動解析 (opt_dft_b3lyp_d_ar2.in)
$comment0
Example of DFT-D (B3LYP-D) calculation of Ar2. First a full geometry optimization, then frequency analysis using all the time B3LYP with empirical dispersion correction (B3LYP-D).
$end$molecule
0 1
Ar
Ar 1 DD = 3.6
$end$rem
JOBTYPE OPT
EXCHANGE B3LYP
CORRELATION LYP
BASIS AUG-CC-PVDZ
EMPIRICAL_DISPERSION TRUE
GEOM_OPT_TOL_GRADIENT 1
$end@@@
$molecule
READ
$end$rem
JOBTYPE FREQ
EXCHANGE B3LYP
CORRELATION LYP
BASIS AUG-CC-PVDZ
EMPIRICAL_DISPERSION TRUE
$end
#003 sampleジョブの一括実行
#!/bin/shfor dir in `find . -type d`; do
cd $dir
for job in *.in; do
# echo $job
qchem -nt 8 $job ${job%in}out
done
cd -
done
