Parameter Optimization Tutorial

Objective and Overview

The objective of this tutorial is to demonstrate how to extend the CHARMM additive biological force fields to drug like molecules. The tutorial is based on the CHARMM force fields, parametrization strategies and future/ongoing developments lecture given at the 2006 MMTSB/CTSB Workshop. Reading the powerpoint presentation from the workshop is suggested prior to attempting the tutorial. The molecule for which parameters will be assigned and developed is shown on the right.


Step one of the process is to break the compound into molecular fragments and create the corresponding model compounds. This process yields indole, phenol and the model compound B shown below. The remainder of the tutorial focuses on obtaining and optimizing parameters for compound B. However, the RTF and parameters for the entire drug molecule, along with that for model compound B, are included in the toppar stream file top_mmtsb_example.str. Note that top_mmtsb_example.str is read after the files top_all27_prot_lipid.rtf and par_all27_prot_lipid.prm located in the toppar subdirectory as performed in the input files given below.


The initial charmm script, gen_model_b.inp, generates B and minimizes the structure in 4 different conformations. In addition, the script writes input files for the Gaussian QM package that may be used to perform minimizations and frequency calculations (gauss subdirectory). Several inputs for the optimization of parameters associated with B are included.

water_model_b.inp: Calculates minimum interaction energies and distances of water with B.

model_b_molvib.inp: Calculates the vibrational spectra including performing normal mode assignments. The data in the resulting output are then compared with results from a QM frequency analysis that may be done in CHARMM using the script model_b_molvib_g03.inp.

model_b_surf_all_one.inp and model_b_surf_all_two.inp calculate several potential energy surfaces for rotation around bonds in B. The two files are run consequtively to obtain surfaces that are offset to zero; this could be performed in one file if so desired. The resulting surfaces may be compared to QM surfaces (see *.map files that include the basis set name mp2_631gs).

For the full drug compound, gen_drug.inp, is used to generate and minimize the compound and, model_2_surf_all.inp, calculates two potential energy surfaces for comparison with QM data (see *

Subdirectory gauss: The subdirectory contains a number of input files for the Gaussian program including those created by gen_model_b.inp and gen_drug.inp. See the 00readme file in that directory for more information.

Specific directions:

1) Copy these files into your working directory, unzip the files and extract the gaussian files from gauss.tar.

2) Evaluating lowest-energy conformations
Generate the fragment "B" and minimize the structure in 4 different conformations:
$CHARMMEXEC < gen_model_b.inp > gen_model_b.out
Gaussian input files are created for each of these 4 conformations and are saved in the gauss directory. These files can be submitted to Gaussian within the gauss directory using the command:
g03 < > model_b_opt_freq_mp2.g03out
(however, running Gaussian is beyond the immediate scope of the MMTSB Workshop tutorials)

3) Evaluating hydration energies and distances
Calculate minimum interaction energies and distances of water molecules to fragment "B":
$CHARMMEXEC < water_model_b.inp > water_model_b.out 
Four PDB files are generated mod1_wat1.pdb through mod1_wat4.pdb corresponding to the optimal positions of water molecules at different hydration sites on the fragment. mod1_wat1.pdb .... O2...HOH
mod1_wat2.pdb .... N3-H3...OHH OUT OF PLANE
mod1_wat3.pdb .... N4...HOH OUT OF PLANE
mod1_wat4.pdb .... C5-H5...OHH OUT OF PLANE

The file model_b_wat.ene contains a summary of the interaction energies and distances of each of these structures along with the ab initio results. This information can be used to evaluate the quality of the existing CHARMM parameters for fragment "B" and decide whether better agreement is desired.

4) Evaluating vibrational spectra
Calculate the vibrational spectra of fragment "B":
$CHARMMEXEC < model_b_molvib.inp > model_b_molvib.out 

Compare the results with the QM frequencies (QM force constants stored in model_b_freq_g03.sec). First, copy model_b_freq_g03.sec to fort.12:
cp model_b_freq_g03.sec fort.12
$CHARMMEXEC < model_b_molvib_g03.inp > model_b_molvib_g03.out 

5) Evaluating the conformational energy barriers
Calculate several potential energy surfaces for rotations around bonds in fragment "B":
$CHARMMEXEC < model_b_surf_all_one.inp > model_b_surf_all_one.out 
Minumum energy structures for each surface are written to: mod1_surf1_final.crd
$CHARMMEXEC < model_b_surf_all_two.inp > model_b_surf_all_two.out 
The lowest-energy structure, model_b_min.crd, is used to properly zero the energy of the surfaces in the following .map files:
The information from these files can then be compared with the QM surfaces obtained from running Gaussian03 files (named: m1_s?_*.com) in the gauss/surfaces directory. Note: Actually, the 00Readme file has an example input file that will "scan" through the desired dihedral angles. This can also be adapted for evaluating bond lengths, angles etc.

6) Evaluating lowest-energy conformations for the full drug molecule
The lowest-energy conformation and two potential energy surfaces for the full molecule can be obtained by:
$CHARMMEXEC < gen_drug.inp > gen_drug.out
$CHARMMEXEC < model_2_surf_all.inp > model_2_surf_all.out
As in step 2, drug_1_min.pdb, the lowest-energy conformation can be compared with that from ab initio calculations by using as the input file for Gaussian03.
As in step 5, and can be compared with potential energy surfaces generated from input files (named: m2_s*_*.com) in the gauss/surfaces directory. Though, again, the "scanning" option in Gaussian, as described in gauss/surfaces/00Readme is a better way to go.
Written by A.D. Mackerell, Jr.