TrypsinActSite – A tool for modelling chymotrypsin
The application is based upon a molecular template which is comprised of a cyclic
hexapeptide(Lys-Xaa-Lys-Asp-Lys-Xbb) with branches (AceGlyAlaSer, AceHid,
AceAsp). It offers quite a lot of choices inside the framework hexapeptide and
Lysine.
Figure 1.

Installation
In order to install the program you just simply unzip it in the folder of your choice
by typing the following command in the shell:
$shell: tar -zxvf tas.tar.gz

Configuration
Before you start “playing” with TAS you must do the following:
Edit the key file lys.key and in the first line put the path of the amber99 force
field parameter file => amber99.prm. For example if the TINKER is installed in the
directory /opt/ you simply type in the first line of the lys.key:
parameters /opt/tinker/params/amber99.prm

Running
1. Command Prompt:
$shell: ./simtrypsin.pl
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## TrypsinActSite - A Tool For Modelling ChymoTrypsin
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Version 1.1 December 2005
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Enter the full path where the parameter directory of TINKER
For instance if /usr/tinker enter /usr
Path: /opt
Enter the version of TINKER you have installed (4.1 or 4.2)
If you have 4.2 press 2 otherwise press 1: 1
Enter the Number of Dynamics Steps to be Taken (fs) : 200000
Enter the Time Step Length in Femtoseconds [1.0] : 1
Enter Time between Dumps in Picoseconds [0.1] : 2
Enter the Desired Temperature in Degrees K [298] : 300
Enter
the
Implicit
Solvation
[ASP/SASA/ONION/STILL/HCT/ACE/GBSA] : SASA
Enter AminoAcid1:ala
Enter AminoAcid2:ala
Choose an option
1. Specific Sequence of Chiralities D/L
2. A symmetrical change of D/L, for instance ( D L D D L D L L L )
3. All combinations of D/L)
Enter (1 or 2 or 3) [2]:1
Enter a specific sequence of chiralities:D D D D D D D
Do you want to enter another one:Y
Enter a specific sequence of chiralities:D D D D D D L
Do you want to enter another one:Y
Enter a specific sequence of chiralities:L L L L L L L
Do you want to enter another one:
You simply press ENTER (Carriage Return) to start the simulation.
Model
2. Input file:
$shell: ./simtrypsin < input.file > output.file &
Example of an input File:
/opt
1
20000
1
1
300
SASA
gly
gly
1
DDDDDDDDD
Y
DDDDDDLLL
Y
LLLLLLLLL
Leave two lines empty !!!
# The installation path of TINKER
# The version of TINKER (4.2)
# The total time of molecular dynamics
# Time interval
# Interval between coordinate/trajectory
# Temperature
# Implicit Solvation model
# Xaa peptide (Figure 1)
# Xbb peptide (Figure 1)
# Choice 1 (specific D/L chirality)
# First peptide
# Y (enter another peptide)
# Second peptide
# Y (enter another peptide)
# Third peptide
TEST RUN.
INPUT
/opt
1
20000
1
1
300
SASA
gly
gly
1
DDDDDDDDD
Y
DDDDDDLLL
Y
LLLLLLLLL
OUTPUT
Peptide RMSd
1
30%
2
5%
3
10%
d1
d2
30% 5%
5% 0%
5% 5%
d3
10%
0%
10%
Description of the test run.
In the first line of the input file the user enters the path where is installed the
TINKER molecular modeling software.
In the second line the user enters the version of the TINKER which is installed. For
instance if it is 4.2 the user just types 2.
Then the total time of molecular dynamics is entered.
The time interval.
The interval between coordinate/trajectory.
The implicit solvation model.
The temperature.
In the next two lines the user inputs the aminoacids which will be positioned in the
Xaa and Xbb positions in the peptide (Figure 1).
In the next line by entering 1 you choose to build a peptide with a specific D/L
chirality.
In the next lines the chiralities of the amino acids (Figure 1) are entered.
If you want to continue entering D/L chiralities you press Y otherwise
ENTER(Carriage Return).
.
The output file shows in the second column the number of the peptide the
percentage of the frames that have RMS under 2.
In the second column the percentage of the frames that have RMS under 2.
In the third column the percentage of the frames that the distance between the
atom of the hydrogen atom of the Histidine (HD1) and the first oxygen atom of the
Aspartic Acid (OD2) is under 3 A.
In the fourth column the percentage of the frames that the distance between the
atom of the hydrogen atom of the Histidine (HD1) and the second oxygen atom of
the Aspartic Acid (OD2) is under 3 A.
In the fifth column the percentage of the frames that the distance between the
hydrogen atom of the Serine (HG) and the nitrogen atom of the Histidine (NE2) is
under 3 A.