Replaces the C-terminus with an ethyl ester group. Replaces the carbonyl group with CH 2. Replaces the C-terminus with a methyl ester group. Replaces the C-terminus with a phenyl ester group. Replaces the C-terminus with a tert-butyl group. Default C-terminal patch for all standard residues.
C-terminal patch for all standard residues; may only be applied after the PSF has been generated. Provides a charged COO - group to unsaturated amino acids. Constructs a disulfide bond between two Cys residues. RTF only. Joins the amino group of Lys with the C-terminus to form a cyclic peptide. Joins two segments to form a peptide bond; links N to C. RFT only. Link patch for proline on the N-terminus links N to C. Converts an L-amino acid to a D-amino acid; may not be used on Pro.
Replaces N-terminus with C 13 H 27 fatty acid amide. Adds a guandino group to the N-terminus; may not be used for Pro. Replaces the peptide nitrogen hydrogen with a methyl group; may not be applied to the first residue. Replaces the peptide nitrogen hydrogen with a hydroxyl group; may not be used on an end residue. Converts an N-terminal glutamic acid to pyroglutamic acid. Replaces the peptide nitrogen with an ester oxygen; may not be applied with Gly as the ester residue; may only be used on non-terminal residues.
Converts Z-dehydrophenylalanine to E-dehydrophenylalanine. Table 48 lists residues and patch residues for nucleic acids. Nucleic acid residue topology files DNA. RTF Name. Places a phosphate at the 5' end after PSF generation.
Patch to add H1 to pyrimidines when using base only. Table 49 lists carbohydrate residues and patch residues in alphabetical order. Residues are not automatically linked together. Links must be explicitly defined. Constructs a phosphate ester to the hydroxyl group at the 2-carbon. There are various quantum mechanical methods available for assigning partial charges in force fields. We will discuss the determination of partial charges in more detail later.
The atoms are divided into groups; with the exception of charged residues such as arginine or glutamate , the net charge of each group is neutral. These entries define the connectivity and the planarity of residues. You may have noticed that although the bonds and atoms are defined in the topology file, the entry is missing angle and dihedral assignments. The angle and dihedrals are never assigned in the topology file.
This should make sense - every 3 connected atoms generates an angle and every 4 generates a dihedral term. The force field excerpts below contain the final missing heavy atom parameters for CYG and can be used as a reference for the assessment of the parameters you develop in the next few exercises. Due to time constraints, for the following exercises, we will only perform semi-empirical calculations. Therefore the final parameter values presented below may differ slightly than the ones you determine.
Theta0: degrees! Ubiquitin is a small and perfectly ordinary protein, making it ideal for an introductory tutorial. Before proceeding to the next step, now is a good time to use your favorite text editor to check for a few things:. Are crystal waters present in the PDB file? In the case of 1UBQ, there are many crystal waters. Ubiquitin is non-enzymatic, though, so the waters are not important for an active site mechanism, for example. Are there any ligands or non-standard residues present in the PDB file?
In the case of 1UBQ, there are no ligands or non-standard residues. Without going into too much detail, non-standard residues are okay so long as the residue name and atom names conform to the corresponding entry in the residue topology file. Are there any residues with missing atoms in the PDB file? In the case of 1UBQ, there are not. If there were, however, you would need to take extra preparation steps beforehand to fix the broken residues before continuing.
Strictly speaking,. The command line execution looks like this:. These selections are fine for this tutorial, but make sure you think very carefully about your choice before picking a force field in your research. You may ask yourself, should I use an all-atom force field or a united-atom force field? Is my force field selection compatible with lipids or small molecules that I want to use? After you have picked the force field and a solvent model compatible with that force field, it is a good idea to read through the output on the screen to make sure there are no Errors or Warnings.
In this case, it looks like there actually was one Warning:. A quick look back at the original PDB file reveals that the four residues at the C-terminus of ubiquitin in 1UBQ were not as well resolved as the rest of the protein. Pdb2gmx noticed that, too, and adjusted the occupancy of each to '1'. This should be okay for now, as the atomic positions of these residues will be refined later in the minimization and equilibration steps. Aside from that one warning, it appears pdb2gmx changed a few residue names and atom names to conform to the names used in the AMBER Ensure that the changes make sense, and it is okay to proceed.
It is very important to know and understand the contents of each file before continuing. Make sure you look through each file until you are able to make sense of the information contained within each. The first line is a title - it is good practice to use a detailed title specific to the system being simulated.
The second line is the number of atoms. The final line contains the box vectors in nanometers. To prepare your system, this tutorial provides the python code below which uses Chimera dockprep functionality to clean the protein and to add missing residues using the Dunbrack rotamer Library.
It is important to notice that hydrogens are not added to the protein in this step because it will be done automatically by a VMD script to avoid issues with atom names differences. On the other hand, for ligands, hydrogens are added using custom forcefield parameters explicitly.
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