# New Solvent Models, Sampling Methods and Maintenance of Amber Software

> **NIH NIH R01** · STATE UNIVERSITY NEW YORK STONY BROOK · 2020 · $304,157

## Abstract

Project Summary
This proposal responds to PA-14-156, Extended Development, Hardening and Dissemination of
Technologies in Biomedical Computing, Informatics and Big Data Science. The goal of this
program is to support the continued development, maintenance, testing and evaluation of
existing software, matching our proposal.
Amber is a very popular software package, used by academic and industry institutions, for simulating
the structural, thermodynamic and kinetic properties of molecular systems. The free version of Amber
has been downloaded by over 10,000 unique users. There are 3,500 citations to the widely adopted
Amber ff99SB protein force field, developed at Stony Brook by PI Carlos Simmerling. The Simmerling
group is one of the six academic labs responsible for leading the Amber software maintenance and
development effort.
Computational molecular dynamics simulations using Amber and other software packages have
become essential counterparts to experimental research for understanding the mechanisms of
biomolecules, and for discovering drugs to inhibit them. The popular virtual screening program called
DOCK interfaces directly with Amber, providing improvements to this widely used program for drug
discovery. Other widely used programs also interface with Amber.
Productivity in our prior funding period was excellent, leading to articles published in PNAS (2),
JACS (3), JCTC (4) and other high-impact journals, with others currently in review. Several new
versions of Amber were released.
We propose here new developments for Amber, addressing two of the most pressing needs of
the field. Aim 1, Solvation: We will incorporate improved solvation models: (a) the SEA semi-
explicit water model and (b) a fast but reasonably accurate Generalized Born implicit water
model. Aim 2, Sampling: We will add fast and targeted sampling methods: (a) variants of the
general tools Hamiltonian exchange and thermal Replica Exchange Molecular Dynamics, (b) the
very fast Kinetic-Loop-Closure and Constrained-Loop-Closure methods for sampling loop
conformations.
Following our practice over the past 20 years, we will openly share our results, parameters and
methods, and incorporate them into the Amber production code for distribution with fully
documented source code, along with full documentation, test cases, and tutorials. New versions
follow an annual release schedule.

## Key facts

- **NIH application ID:** 9974519
- **Project number:** 5R01GM107104-08
- **Recipient organization:** STATE UNIVERSITY NEW YORK STONY BROOK
- **Principal Investigator:** CARLOS SIMMERLING
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $304,157
- **Award type:** 5
- **Project period:** 2013-08-01 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9974519

## Citation

> US National Institutes of Health, RePORTER application 9974519, New Solvent Models, Sampling Methods and Maintenance of Amber Software (5R01GM107104-08). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/9974519. Licensed CC0.

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