The ARM Web Interface ver. 0.1

Created by Luca De Vico

Based on the ARM protocol developed by the Massimo Olivucci's group

If using this interface, please cite: "Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology" J. Chem. Theory Comput., 2016, 12, pp 6020-6034

This web interface is still a prototype. Stay tuned for further improvements.

Please, provide a pdb file with already included counterions. In the future, the interface will include a service to compute and position the number of necessary counterions, the discovery of the cavity residues, the possibility of adding water molecules, and relax the protein backbone.

Please enter or accept values
Upload a pdb file containing a retinal
Select a file: Note: for the moment the interface will NOT check the correctness of the uploaded pdb file
Enter a valid email
Your email: Note: all communication will be through this email

Enter the information about the retinal and its surrounding
Retinal-bound lysine residue ID Arm automatic choice Manual choice
Type of retinal all-trans, charge +1 11-cis, charge +1 13-cis, charge +1 all-trans, charge 0
How many cavity residues? Note: it is mandatory to specify a number of residues!!
Cavity residues:

Do you wish to introduce also site mutations? (we strongly recommend less than 4)
Yes No
How many mutations?
From To Residue's number

Enter the information about the dynamics calculations
The calculation will use crystal water molecules by default

Simulated annealing On hydrogen atoms within a fixed radius from the retinal On all hydrogen atoms No annealing

Select what do you want to do
MM minimization on cavity sidechains MD on cavity hydrogen atoms MD on cavity sidechains MD on all hydrogen atoms MD on all sidechains

Do you want to move the retinal? Yes No

The calculation will NOT relax the backbone by default

What is the production temperature (Kelvin)?
Do you want to heat the system before the MD? Yes No Insert the heating phase time (ps)
Insert the equilibration phase time (ps) Insert the production phase time (ps)
Insert how many dynamics to run
Enter the information about the CAS calculations
Do you want to use the nearest-to-average frame? Yes No
Do you want to use microiterations? Yes No
Ready to try ARM?