Setup FF from CHARMM’s rtf and prm¶
This page shows how DL_FIELD can be used to extract FF information from rtf and prm files to setup FF models for DL_POLY and Gromacs.
The rtf (residue topology file) and prm (parameter file) are standard CHARMM FF file formats that are produced from many third-party sources for simulation and modelling using packages such as CHARMM and NAMD.
For example, the LigParGen is an FF web server interface (http://zarbi.chem.yale.edu/ligpargen/) that can automatically generate OPLSAA models for organic molecules, such as drug molecules or ligands with proteins and DNA.
DL_FIELD can transcribe these FF models into DL_POLY and Gromacs files, via the Charmm’s rtf and prm files produced by LigParGen. This is done as follows, by using ascorbic acid as an example:
Example procedure
When reading in CHARMM’s rtf and prm files, DL_FIELD will convert the FF data and create a corresponding udff file called dlf_charmm.udff file.
Steps below illustrate the possible workflow procedures to setup FF models from rtf and prm files.
Step 1: Visit LigParGen site (shown above) and use ascorbic_acid.pdb as the input structure for the LigParGen server and select the 1.14*CM1A-LBCC charge model.
Step 2: Upon successful run, you are given several Download options. Select and download PRM and RTF files for CHARMM/NAMD.
Step 3: Rename these prm and rtf files into something sensible, such as ascorbic_acid.rtf and ascorbic_acid.prm. However, this step is optional.
At DL_FIELD side:
Step 4: Specify the rtf and prm files in the dl_f_path file (see below).
# paths
library = lib/
solvent = solvent/
output = output/
# paths and filenames
control = dl_field.control5
charmm_rtf = ascorbic_acid.rtf opls2005
charmm_prm = ascorbic_acid.prm opls2005
The COMPONENT FILE TYPEs charmm_rtf and charmm_prm indicate the location of the rtf and prm files and the associated FF scheme, which is OPLS2005.
Warning
Although rtf and prm are the original file formats for CHARMM software, in this case, the LigParGen produces FF data for OPLS scheme. For this reason, the FF scheme must be specified as OPLS2005 in dl_f_path and not some CHARMM FF schemes.
Step 5: Run DL_FIELD. The following message will be shown on the screen:
...
...
Processing Charmm rtf file: pentanoic_acid.rtf...
Completed.
Processing Charmm prm file: pentanoic_acid.prm...
Completed.
The udff file dlf_charmm.udff has been created.
Only file format conversions had been carried out.
The rest of the control options have been ignored.
If you want conversion to DL_POLY FIELD file in a single step,
you can insert dlf_charmm.udff and dlf_charmm.pdb as the udff and input files.
prior to file format conversion.
Program executed successfully. Thank you for using DL_FIELD.
As the message above shown, all control options will be ignored. The only output file would be the dlf_charmm.udff file, which contains all the FF information extracted from the rtf and prm files.
However, file format conversions and FF model set up processes can be combined by carrying out the additional steps as follows:
Step 6: Ensure the correct residue labels are used in the intput PDB file. From the rtf file, the ascorbic acid molecule is given the RESIdue name UNK. This would be the same label for the MOLECULE_KEY in dlf_charmm.udff file. This label must be included in the PDB file (at column 18-21 as shown below), so that DL_FIELD would know which MOLECULE template to use when setting up the FF.
REMARK PDB file
HETATM 1 CT UNK 1 0.532 0.696 0.513 1.00 0.00 C
HETATM 2 CT UNK 1 1.113 -0.707 0.463 1.00 0.00 C
HETATM 3 HC UNK 1 1.181 1.391 1.091 1.00 0.00 H
HETATM 4 OH UNK 1 -0.719 0.667 1.173 1.00 0.00 O
HETATM 5 HC UNK 1 0.376 1.116 -0.505 1.00 0.00 H
HETATM 6 HC UNK 1 0.965 -1.221 1.442 1.00 0.00 H
HETATM 7 OH UNK 1 0.426 -1.459 -0.512 1.00 0.00 O
…
…
Step 7: Insert the udff filename dlf_charmm.udff and the input configuration file in DL_FIELD control file, as shown below.
Control file title.
1 * Construct DL_POLY output files
none * chemsh interface (for QM/MM), gromacs or none
opls2005 * Type of force field require (see list below for choices).
kcal/mol * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal * Conversion criteria (strict, normal, loose)
1 * Bond type (0=default, 1=harmonic , 2=Morse)
1 * Angle type (0=default, 1=harmonic, 2=harmonic cos)
dlf_charmm.udff * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
ascorbic_acid.pdb * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
0 40 molecules 9.0 * Solution Maker: on/off, density, unit, cutoff)
...
...
Step 8: Run DL_FIELD. Once a dlf_charmm.udff file is created, DL_FIELD proceeds to read in the input configuration file and setup the FF model as usual.
Note
If you want to setup Gromacs FF files, remember to insert gromacs keyword in the control file.