Computational Drug Discovery and Design

Refs. [22, 23]). We performed MD simulation using NAMDv2.8

package with the CHARMM22/CMAP biomolecular force-field

[24, 25]. The topology and parameter files for the ligand were

generated using SwissParam web server, which provides topologies

and parameters based on the Merck molecular force field (MMFF)

and is compatible with the CHARMM force field [26]. Apo form of

A2AAR was obtained by minimizing the inactive A2AAR structure

after the removal of the bound antagonist. The water layer was

prepared using the Helmut Grubmuller’s SOLVATE 1.0 program,

followed by the merging of protein and water layer. Subsequently,

the water molecules surrounding the TM-regions were removed.

Since GPCRs are embedded in a lipid bilayer system, it is essential

to mimic native-like conditions, which remain a crucial aspect in

membrane simulations. We implemented the POPC membrane

building procedure using a plug-in available athttp://www.ks.

uiuc.edu/Research/vmd/plugins/membrane/ to do the entire

process in VMD [27]. Some groups have made few preequilibrated

membrane systems available (Table1), which may speed up the

process of membrane building protocol. To construct an explicit

membrane-protein system, the TM region of A2AAR was predicted

based on the Orientations of Proteins in Membranes (OPM)

Table 1
List of various software packages/webservers for membrane building.

Program/Server

Output compatibility with simulation

packages Source

Automated Topology

Builder (ATB)

GROMACS, GROMOS, LAMMPS https://atb.uq.edu.au/

CHARMM-GUI

Membrane Builder

CHARMM, GROMACS, AMBER,

GENESIS, OPENMM, CHARMM/

OPENMM

http://www.charmm-gui.

org/?doc¼input/membrane

ChemSite Pro® Information N/A ChemSW®

CELLmicrocosmos 2.2

MembraneEditor

(CmME)

GROMACS http://www.cellmicrocosmos.

org/index.php/cm2-project

MemBuilder II (Beta

Ver.)

CHARMM, GROMACS, AMBER http://bioinf.modares.ac.ir/

software/mb2/builder.php

MemGen Not restricted http://memgen.uni-

goettingen.de/

Packmol AMBER, GROMACS, MOLDY http://www.ime.unicamp.br/

martinez/packmol

VMD Membrane-Plugin CHARMM http://www.ks.uiuc.edu/

Research/vmd/plugins/

membrane/

Molecular Dynamics Approach for Investigation of GPCR Allostery 459