QC-partial-charges-AMBER

A step-by-step procedure for calculating partial atomic charges compatible with the AMBER General Force Field (GAFF) uses quantum chemical calculations with GAMESS and Restrained Electrostatic Potential (REsP) fitting via Antechamber.

System Setup

First, you need a PDB or XYZ file of your molecule. If the structure is unavailable, you can easily build it using molecular editing and visualization software such as Avogadro, VMD, PyMOL, etc. Below is an example of a biomolecule PDB file used in this tutorial.

 QC-partial-charges-AMBER/examples/biobinder_molecule/01-structure/BB14.pdb 

Quantum Calculation Setup

We used the open-source GAMESS-US package for quantum calculations. To prepare a proper GAMESS input file, we recommend you review the input file format and available options in GAMESS-US.
Here, we walk through a few options used for calculating partial charges. The directory below provides the GAMESS input file used in this tutorial:

 QC-partial-charges-AMBER/examples/biobinder_molecule/02-GAMESS-input-file/bb14-b3lyp.inp  

On the basis of AMBER suggestions, the 6-31G* basis set is chosen, which is mentioned in the command below

 $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END  

The $control group defines the overall quantum calculation method, job type, charge, multiplicity, and coordinate system. For example:

$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE DFTTYP=B3LYP MULT=1 COORD=UNIQUE
        MOLPLT=.TRUE. MAXIT=50 $END 

The system's net charge is defined by the ICHARG command, which has a default of zero. The default value will be implemented if ICHARG is not specified.

The MULT keyword specifies the spin multiplicity of the electronic state. The default value is 1, which corresponds to a singlet state, meaning all electrons are paired (no unpaired electrons). For systems with at least one unpaired electron, the user must specify the multiplicity.

The SCFTYP keyword is used to specify the type of self-consistent field (SCF) wavefunction. Several options are available, but the two most common are RHF (Restricted Hartree-Fock) and UHF (Unrestricted Hartree-Fock). RHF is typically used for closed-shell systems, where all electrons are paired, and UHF is used for open-shell systems that contain unpaired electrons. The maximum number of SCF iterations is specified by MAXIT=50. The calculation will terminate with an error if the SCF procedure does not converge within 50 iterations. To activate the direct SCF, which means calculating integrals rather than storing them all in a memory disk, you need to use DIRSCF=.TRUE. in the $SCF group as:

$SCF DIRSCF=.TRUE. $END 

The DFTTYP keyword performs density functional theory (DFT) calculations. The AMBER force field recommends using B3LYP, a widely used hybrid functional that combines five components: Becke, Slater, and Hartree-Fock (HF) exchange (B3), along with LYP and VWN5 correlation functionals.

RUNTYP=OPTIMIZE is used to perform energy minimization. If you plan to calculate partial charges without optimizing the geometry, use RUNTYP=ENERGY instead. The $STATPT group controls the settings for geometry optimization:

$STATPT OPTTOL=0.0001 NSTEP=200 PROJCT=.FALSE. $END 

where the OPTTOL keyword specifies the gradient convergence tolerance, the NSTEP keyword specifies the maximum number of steps, and PROJCT controls whether to project out translation and rotation from the optimization gradient.

The COORD=UNIQUE provides Cartesian coordinates in the $DATA block.

The MOLPLT=.TRUE. enables molecular orbital output for visualization.

The $SYSTEM group sets options related to memory usage and parallel computation. Please review the docs-input.txt file of the GAMESS-US package.

$SYSTEM MWORDS=100 MEMDDI=500 PARALL=.TRUE. $END

The $ELPOT and $PDC groups control the generation of electrostatic potential (ESP) data for computing partial atomic charges.

$ELPOT IEPOT=1 WHERE=PDC $END
$PDC PTSEL=CONNOLLY $END 

IEPOT=1 activates the calculation of the ESP on a grid, while WHERE=PDC specifies where to place the grid points for the ESP calculations. PDC stands for Potential Derived Charges, and the group determined the method of computing ESP-based atomic charges. Following the AMBER recommendation, the CONNOLLY method is selected. In this approach, grid points are distributed over a set of fused van der Waals spheres using a surface generation algorithm developed by Michael Connolly.

At the end of the GAMESS input file, the $DATA group must be identified, which specifies the title, symmetry, and atomic coordinates.

 $DATA 
Title
C1
O     8.0     1.0669000000   0.3186900000  -1.1464000000
O     8.0    -7.0195700000   1.3754900000  -0.4785000000
O     8.0     4.7814100000   1.0959300000  -0.1638200000
O     8.0     6.2342900000   2.4721300000   0.5723600000
C     6.0     0.4666300000  -0.8737300000  -0.6069900000
                  .
                  .
                  .
 $END

The Title line is a user-defined title line. The C1 indicates no symmetry. After that, the atom name, atomic number, and Cartesian coordinate (in Å) are defined at each line.

If the simulation is converged, a .dat format file containing all information about the EPS calculations will be generated.

/examples/biobinder_molecule/02-GAMESS-input-file/bb14-b3lyp.dat

In the following section, we introduce our in-house C++ script that converts this data into the input files required by the RESP package.

GAMESS output to REsP input

To run RESP—an AMBER tool accessed via Antechamber—we have developed an in-house C++ script named GAMESS_to_RESP. This program converts the GAMESS .dat output file into the required REsP input files: esp.dat and resp.in.

To install the GAMESS_to_RESP:

cd GAMESStoRESP directory
make

To uninstall:

make clean

To execute the program, run the GamessToResp executable from the command line:

[pathtocode]/GAMESStoRESP/GamessToResp

You need to create a gamess-resp.in file and specify the following parameters: - gamess-dat-file: Path and filename of the GAMESS-generated .dat file. - qc_min: Indicates whether quantum chemical minimization was performed before ESP calculation (YES or NO). - net_charge: The net charge of the system.

A sample gamess-resp.in file can be found in the directory below:

QC-partial-charges-AMBER/GAMESStoRESP/gamess-resp.in

REsP fitting

The REsP fitting tool is part of the Antechamber package in AMBER. To run REsP, you need to install the Antechamber package.

AMBER also provides an excellent tutorial that explains in detail the parameters required in the resp.in file.

We provide two-step REsP fitting in the following directories for the biomolecule:

QC-partial-charges-AMBER/examples/biobindermolecule/03-RESP-inputfile-step01/

QC-partial-charges-AMBER/examples/biobindermolecule/03-RESP-inputfile-step02/

Citation

If you use this code in your work, please cite:

Faramarz Joodaki, Michael L. Greenfield. GAMESStoRESP: A tool for converting GAMESS outputs for RESP charge fitting. GitHub repository, 2025.

BibTeX: ```bibtex @misc{fjoodaki2025gamesstoresp, author = {Faramarz Joodaki and Michael L. Greenfield}, title = {GAMESS_to_RESP: A tool for converting GAMESS outputs for RESP charge fitting}, year = 2025, publisher = {Zenodo}, url = {https://doi.org/10.5281/zenodo.15795500}, doi = {10.5281/zenodo.15795500}, note = {Archived GitHub repository at Zenodo} }