Uploads to PyRED | Computational Chemistry Resources

First things first: PyRED knows what it wants. If it wants something titled a particular way, it will only accept things with that particular title. So treat PyRED like the royalty it is and don’t disobey it. Second things second: if your school has a Gaussian license, you can apply for an academic account that will allow you to run the quantum calculation with Gaussian (you don’t have to use Gaussian, in this instance, so don’t worry).

Tip: PyRED’s account registration is finicky, and the Captcha is intense. Pay attention to the differences between uppercase and lowercase letters when making an account, and save your assigned login and password, since you don’t get to change it.

Nucleotide Fragment Generation

PyRED creates parameters for nucleotides in fragments.

For monophosphates, you’ll build in two fragments: the capped phosphate with an O5’, and the nucleotide out to O5’ with a hydrogen cap. PyRED will build these two structures together, with the specified connectivity information in Project.config.

Dimethylphosphate Portion of PDB (Mol_red1.pdb)

ATOM      1  C1  DMP     1       1.100   0.000   0.000
ATOM      2  H11 DMP     1       0.000   0.000   0.000
ATOM      3  H12 DMP     1       1.476   1.034   0.000
ATOM      4  H13 DMP     1       1.476  -0.484   0.913
ATOM      5  O3' DMP     1       1.524  -0.687  -1.135  
ATOM      6  P   DMP     1       3.138  -0.847  -1.398  
ATOM      7  O1P DMP     1       3.811   0.378  -0.942  
ATOM      8  O2P DMP     1       3.281  -1.435  -2.738  
ATOM      9  O5' DMP     1       3.475  -2.001  -0.280
ATOM     10  C2  DMP     1       3.096  -3.315  -0.544
ATOM     11  H21 DMP     1       2.018  -3.403  -0.661
ATOM     12  H22 DMP     1       3.568  -3.689  -1.444
ATOM     13  H23 DMP     1       3.401  -3.925   0.302

Example Project.config

# Provide informative titles
MOLECULE1-TITLE        = Dimethylphosphate
MOLECULE2-TITLE        = NucleotideOfInterest

# Providing the total charge for molecule 1 is mandatory
MOLECULE1-TOTCHARGE    = -1
# Providing the total charge for molecule 2 is not mandatory
MOLECULE2-TOTCHARGE    =  0

# Define two inter-mcc between molecule 1 and molecule 2
MOLECULE-INTER-MCC1    = 0.0 | 1 2 |  1  2  3  4 | 1 2
MOLECULE-INTER-MCC1    = 0.0 | 1 2 | 10 11 12 13 | 3 4

In the Project.config file, the lines with MOLECULE-INTER-MCC1 describe where the connections need to be made between the two compounds. In the example, molecule 1’s 1 2 3 4 | 1 2 refers to C1, H11, H12, H13, H12, and H13. Molecule 2’s | 10 11 12 13 | 3 4 refers to C3’, H3’, C4’, H4’, O3’, and H3T.

Example `System.config`

FFPARM = AMBERFF99SB

Using the Job Information

After the job has completed (you should get an email), you can download the project folder. This folder will have substantially more information if the job completes successfully! 😃

Completed Jobs

Inside the project folder (named P with a string of numbers), you can find the mol2 file by entering the Data-R.E.D.Server/. If you ran a job split into multiple Mol_red files that needed to have intermolecular connections, then enter the Mol_MM folder, followed by the INTER folder. The important mol2 file(s) should be in that folder. Check that the structure optimized as you anticipated by viewing the mol2 in VMD. You should also check that the assigned AMBER atom types make sense.

Note: Chimera will open mol2 files, but they’ll have weird spheres that can be confusing to interpret.

The frcmod files can be found from the project folder and then entering Data-R.E.D.Server/Data-Default-Proj. The frcmod.known is anything that PyRED found parameters for. The missing parameters are listed in frcmod.unknown, and it will usually mark if it thinks they are optional. You can find missing parameters in publications, or by using parmchk or parmchk2 from AMBERTools.

$ parmchk2 -i Mol-sm_m1-c1.mol2 -f mol2 -o my_new_residue.frcmod

Jobs that Errored Out

In the project file, there should be a file that is titled similarly to R.E.D.-Server-3672.master1.q4md-forcefieldtools.org.log. This log should have more information on why the job failed. If not, the Gaussian log files should help you debug the problem.