Mixed Solvent MD System Builder 1.0

Developed by Dr. Sean's Team of Drug Design and Discovery
Upload protein structure (PDB file)
Force Field and Box
Box Setup Mode:
(Polar amide; strong hydrogen bond donor. Captures strong hydrogen bonding interactions.)
(Highly polar solvent; enhances membrane permeability. Often used with water, small-molecule probes, or aromatic probes to enhance detection of both polar and hydrophobic cryptic pockets.)
(Polar protic solvent; hydrogen bond donor. Captures polar protic interactions.)
(Low-polarity solvent. Captures small hydrophobic interactions.)
(Polar aprotic solvent; captures hydrophilic interactions and acts as a hydrogen bond donor.)
(Mimics positively charged environments.)
(Mimics negatively charged environments.)
(Model compound for peptide backbone hydrogen bonding; mimics peptide substrate interactions in cryptic pockets.)
(Hydrophobic aromatic solvent; captures hydrophobic aromatic interactions.)
(Nonpolar aromatic solvent; captures nonpolar aromatic interactions.)
(Moderately polar aromatic solvent; captures hydrophobic aromatic interactions.)
(Aromatic moiety; mimics tryptophan side chains and captures hydrophobic interactions.)
(Nitrogen-containing aromatic base; captures aromatic interactions and serves as a soluble aromatic probe.)
Add Ions and Salt

How to Use This Tool

To perform molecular dynamics simulations using the AMBER engine, please use the .crd and .top files located in the amber/ folder of the downloaded archive. These files are converted from the original GROMACS input and are ready for direct use in AMBER workflows. Amber test files