Protein-ligand HTMD simulation

Annotation:

StepAnnotation
Step 1: Get PDB file
6hhr
Step 2: Input dataset
select at runtime
Step 3: Search in textfiles
Output dataset 'output' from step 1
Don't Match
Perl
HETATM
case insensitive
0
0
text file (for further processing)
Step 4: Compound conversion
Output dataset 'output' from step 2
Sybyl Mol2 format (mol2)
False
False
False
True
False
7.0
False
Empty.
No unique filter
Step 5: GROMACS initial setup
Output dataset 'output' from step 3
TIP3P
AMBER99SB
False
False
Step 6: Generate MD topologies for small molecules
Output dataset 'file_outputs' from step 4
0
1
gaff
True
Step 7: Merge GROMACS topologies
Output dataset 'output1' from step 5
Output dataset 'output' from step 6
Output dataset 'output2' from step 5
Output dataset 'gro_output' from step 6
Step 8: GROMACS structure configuration
Output dataset 'complex_gro' from step 7
GRO file
Yes
1.0
Triclinic
False
Step 9: GROMACS solvation and adding ions
Output dataset 'output' from step 8
Output dataset 'complex_top' from step 7
SPC (generic three-point model)
Yes, add ions
False
Step 10: GROMACS energy minimization
Output dataset 'output1' from step 9
Output dataset 'output2' from step 9
Use default (partially customisable) setting
Steepest descent algorithm.
Generate a pair list with buffering.
Fast smooth Particle-Mesh Ewald (SPME) electrostatics.
1.0
1.0
1.0
50000
1000.0
0.01
True
Step 11: GROMACS simulation
Output dataset 'output1' from step 10
Output dataset 'output2' from step 9
Inputs:
select at runtime
Output dataset 'output3' from step 5
select at runtime
Outputs:
Return .xtc file (reduced precision)
Return .gro file
Produce CPT output
Produce EDR output
No XVG output
No TPR output
Settings:
Isothermal-isochoric ensemble (NVT)
Use default (partially customisable) setting
A leap-frog algorithm for integrating Newton's equations of motion.
All bonds (all-bonds).
Generate a pair list with buffering.
Fast smooth Particle-Mesh Ewald (SPME) electrostatics.
300
0.002
1000
1.0
1.0
1.0
50000
True
Step 12: GROMACS simulation
Output dataset 'output1' from step 11
Output dataset 'output2' from step 9
Inputs:
Output dataset 'output5' from step 11
Output dataset 'output3' from step 5
select at runtime
Outputs:
Return .xtc file (reduced precision)
Return .gro file
Produce CPT output
Produce EDR output
No XVG output
No TPR output
Settings:
Isothermal-isobaric ensemble (NPT)
Use default (partially customisable) setting
A leap-frog algorithm for integrating Newton's equations of motion.
All bonds (all-bonds).
Generate a pair list with buffering.
Fast smooth Particle-Mesh Ewald (SPME) electrostatics.
300
0.002
1000
1.0
1.0
1.0
50000
True
Step 13: GROMACS simulation
Output dataset 'output1' from step 12
Output dataset 'output2' from step 9
Inputs:
Output dataset 'output5' from step 12
Output dataset 'output3' from step 5
select at runtime
Outputs:
Return .xtc file (reduced precision)
Return .gro file
No CPT output
No EDR output
No XVG output
No TPR output
Settings:
Isothermal-isochoric ensemble (NVT)
Use default (partially customisable) setting
A leap-frog algorithm for integrating Newton's equations of motion.
No constraints except for those defined explicitly in the topology (none).
Generate a pair list with buffering.
Fast smooth Particle-Mesh Ewald (SPME) electrostatics.
300
0.002
1000
1.0
1.0
1.0
1000000
True