Incorporate CGenFF Molecules

DruGUI can also be used for setting up a system containing other probe molecules, which can be obtained from the CHARMM General Force Field. This cannot be achieved using the DruGUI window interface but DruGUI also has a command utility drugui that can be run using the Tk Console in VMD as we show below.

Likewise, simulations using these probes cannot be analysed using the DruGUI interface but we can do this using command line tools instead. Please contact us for assistance with this analysis. We will update the tutorial with instructions for this soon.

In VMD, open and type the following command to prepare a system with a probe composition of 30% imidazole, 30% isopropanol, and 10% of each of acetate, acetamide, isopropylamine, and isobutane:

% drugui mdm2.psf mdm2.pdb -IPRO 30 -IMID 30 -ACTT 10 -ACAM 10 -IPAM 10 -IBTN 10

There is a large selection of potential probes you can incorporate in a simulation. You can get a list of them by running drugui command, which will print:

% drugui
Info) Usage: drugui <psffile> <pdbfile> [options]
Info)
Info) Options:
Info)     -probes <Yes/no>
Info)       (use default probe mixture; see below)
Info)     -PROBE <percentage>
Info)       (probe type and percentage, e.g. -IPRO 80 -ACET 10 -IPAM 10)
Info)     -prefix <outname>
Info)       (data will be written to outname.psf/outname.pdb/etc.)
Info)     -outdir <directory>
Info)       (data will be written into specified directory, default is .)
Info)     -rotate <yes/No>
Info)       (rotate molecule to minimize water volume)
Info)     -padding <distance>
Info)       (minimum solvent box padding in all directions, default is 6 A)
Info)     -boundary <distance>
Info)       (minimum distance between water/probe and solute, default is 2.4 A)
Info)     -neutral <Yes/no>
Info)       (add counter ions, chloride or sodium, to make the system neutral)
Info)     -lipid <yes/No>
Info)       (system is solvated by considering lipid bilayer in xy plane)
Info)     -nsim <number>
Info)       (number of independent simulations, default 0)
Info)     -simlen <ns>
Info)       (length of individual simulations in ns)
Info)     -constrain <Heavy/calpha>
Info)       (which protein atoms to contraint in equilibration step)
Info)     -parameter <filename>
Info)       (additional parameter files; multiple occurrence is handled)
Info)
Info) Available probes -RESI [default_percentage] (name, charge, source)
Info)
Info) Core probes
Info)     -IPRO 70% (isopropanol, 0.0e, PBDA)
Info)     -ACAM 10% (acetamide, 0.0e, PBDA)
Info)     -ACTT 10% (acetate, -1.0e, PBDA)
Info)     -IPAM 10% (isopropylamine, 1.0e, PBDA)
Info)     -IBTN (isobutane, 0.0e, PBDA)
Info)     -IMID (imidazole, 0.0e, PBDA)
Info)
Info) Polar probes
Info)     -PRO2 (2-propanol, 0.0e, CGenFF)
Info)     -GLYN (glycine, 0.0e, CGenFF)
Info)     -ACEH (acetic acid, 0.0e, CGenFF)
Info)     -ACEM (acetamide, 0.0e, CGenFF)
Info)     -PRAM (propionamide, 0.0e, CGenFF)
Info)     -NMA (N-methylacetamide, 0.0e, CGenFF)
Info)     -ACO (acetone, 0.0e, CGenFF)
Info)     -TFE (trifluoroethanol, 0.0e, CGenFF)
Info)     -MP_0 (neutral methylphosphate, 0.0e, CGenFF)
Info)     -UREA (urea, 0.0e, CGenFF)
Info)     -MSAM (methanesulfonamide, 0.0e, CGenFF)
Info)     -MMSM (N-methylmethanesulfonamide, 0.0e, CGenFF)
Info)     -MMST (methyl methanesulfonate, 0.0e, CGenFF)
Info)     -DMSN (dimethyl sulfone, 0.0e, CGenFF)
Info)     -MESN (methyl ethyl sulfone, 0.0e, CGenFF)
Info)     -DMSO (dimethylsulfoxide, 0.0e, CGenFF)
Info)     -2PDO (2-pyrrolidinone, 0.0e, CGenFF)
Info)     -TMAO (trimethylamine N-oxide, 0.0e, CGenFF)
Info)
Info) Hydrophobes
Info)     -IBUT (isobutane, 0.0e, CGenFF)
Info)     -BUTA (butane, 0.0e, CGenFF)
Info)     -EMS (ethylmethylsulfide, 0.0e, CGenFF)
Info)     -DMDS (dimethyldisulfide, 0.0e, CGenFF)
Info)     -DFET (difluoroethane, 0.0e, CGenFF)
Info)     -TFET (trifluoroethane, 0.0e, CGenFF)
Info)     -DCLE (1,1-dichloroethane, 0.0e, CGenFF)
Info)     -TCLE (1,1,1-trichloroethane, 0.0e, CGenFF)
Info)
Info) Negatively charged
Info)     -ACET (acetate, -1.0e, CGenFF)
Info)     -PROA (propionic acid, -1.0e, CGenFF)
Info)     -CO3 (ionized carbonate, -2.0e, CGenFF)
Info)     -MP_1 (anionic methylphosphate, -1.0e, CGenFF)
Info)     -MP_2 (dianionic methylphosphate, -2.0e, CGenFF)
Info)     -MSNA (methyl sulfonate, -1.0e, CGenFF)
Info)     -ESNA (ethyl sulfonate, -1.0e, CGenFF)
Info)
Info) Positively charged
Info)     -GUAN (guanidinium, 1.0e, CGenFF)
Info)     -MGUA (methyl-guanidinium, 1.0e, CGenFF)
Info)     -AMDN (amidinium cation, 1.0e, CGenFF)
Info)
Info) 5-membered rings
Info)     -IMIA (imidazole, 0.0e, CGenFF)
Info)     -IMIM (imidazolium, 1.0e, CGenFF)
Info)     -MIMI (4-methylimidazole, 0.0e, CGenFF)
Info)     -THAZ (thiazole, 0.0e, CGenFF)
Info)     -TRZ4 (triazole124, 0.0e, CGenFF)
Info)     -PYRL (pyrrole, 0.0e, CGenFF)
Info)     -FURA (furan, 0.0e, CGenFF)
Info)     -THIP (thiophene, 0.0e, CGenFF)
Info)     -OXAZ (oxazole, 0.0e, CGenFF)
Info)     -ISOX (isoxazole, 0.0e, CGenFF)
Info)     -ISOT (isothiazole, 0.0e, CGenFF)
Info)     -PYRZ (pyrazole, 0.0e, CGenFF)
Info)     -OXAD (oxadiazole123, 0.0e, CGenFF)
Info)     -2HPR (2H-pyrrole, 0.0e, CGenFF)
Info)     -2PRL (2-pyrroline, 0.0e, CGenFF)
Info)     -2PRZ (2-pyrazoline, 0.0e, CGenFF)
Info)     -2IMI (2-imidazoline, 0.0e, CGenFF)
Info)     -PRLD (pyrrolidine, 0.0e, CGenFF)
Info)     -3PRL (3-pyrroline, 0.0e, CGenFF)
Info)     -PRLP (pyrrolidine protonated, 1.0e, CGenFF)
Info)     -3PRP (3-pyrroline protonated, 1.0e, CGenFF)
Info)     -2PRP (2-pyrroline protonated, 1.0e, CGenFF)
Info)     -2IMP (2-imidazoline protonated, 1.0e, CGenFF)
Info)     -2HPP (2H-pyrrole protonated, 1.0e, CGenFF)
Info)     -3HPR (3H-pyrrole, 0.0e, CGenFF)
Info)     -CPDE (cyclopentadiene, 0.0e, CGenFF)
Info)     -DIOL (1,3-Dioxolane, 0.0e, CGenFF)
Info)     -IMDP (Imidazolidine protonated, 1.0e, CGenFF)
Info)     -PRZP (Pyrazolidine protonated, 1.0e, CGenFF)
Info)     -2DHF (2,3-dihydrofuran, 0.0e, CGenFF)
Info)     -MCPE (methylcyclopentane, 0.0e, CGenFF)
Info)     -OXD4 (oxadiazole124, 0.0e, CGenFF)
Info)     -THF (tetrahydrofuran, 0.0e, CGenFF)
Info)     -THFM (Methyl-tetrahydrofuran, 0.0e, CGenFF)
Info)     -THFO (3'-hydroxyl-tetrahydrofuran, 0.0e, CGenFF)
Info)     -CPEN (cyclopentane north types, 0.0e, CGenFF)
Info)     -CPES (cyclopentane south types, 0.0e, CGenFF)
Info)
Info) 6-membered rings
Info)     -BENZ (benzene, 0.0e, CGenFF)
Info)     -PY01 (4H-Pyran, 0.0e, CGenFF)
Info)
Info)
Info) Notes:
Info)     - Passing "y" or "n" (case-insensitive) is sufficient for applicable options.
Info)     - When probe types are specified, probe percentages must add up to 100.
Info)     - When probe is "no", only water (and ions) will be added.
Info)     - Water segment name prefix is "WT".
Info)     - Ion segment name is "ION".
Info)     - Input molecule dimensions are used to determine size of the solvation box.
Info)     - When specified, all atoms of the system is rotated by 10 degree increments.
Info)     - Sodium and chloride ions are used to neutralize the system.
Info)     - Minimum distances from solute and between ions are set to 5 A.