GROMACS Modify Force Field and Increase Residue Tutorial

PCA is used for exploratory data analysis and building predictive models. It is usually used for dimensionality reduction. The method is to project each data point onto only the first few main components to obtain lower-dimensional data while retaining as many data changes as possible. It can be seen from any target that the principal component is the eigenvector of the data covariance matrix. Therefore, the principal components are usually calculated by the eigen decomposition of the data covariance matrix or the singular value decomposition of the data matrix. PCA is the simplest multivariate analysis based on real feature vectors and is closely related to factor analysis. Factor analysis usually includes more domain-specific assumptions about the underlying structure and solves the matrix with slightly different eigenvectors.

Tutorial to modify the force field

In GROMACS 4.5 and later, the best way to modify the force field is to first copy the existing force field directory to your working directory, for example:

cp -r $GMXLIB/residuetypes.dat $GMXLIB/amber99sb.ff.

Then modify the files in the working directory. When pdb2gmx runs, it will find the original and modified versions that come with the system. You can select the modified version from the list given, or use the pdb2gmx -ff option to replace the system with the version of.

Tutorial for adding new residue

Non-standard residues are very cumbersome to do, and there are three main ways to deal with them:

  • For simple non-standard residues, such as methylation, you can manually combine the topology by yourself and modify the atom number.
  • More complicated, you can use AMBER, and then acpype directly to get the topology. For AMBER's tutorial on handling non-standard residues, please refer to Calculation using non-standard residue(s)
  • The most common method is to modify the library files involving residues in the force field, such as rtp, hdb files. After doing this, you can use pdb2gmx to process it.

No matter which method is used, the premise is to obtain the topological file of non-standard residues and ensure that it is correct, and the steps depend on the force field you use. For some parameters, you may have to refer to the original literature or fit by yourself to get the format and parameters of the .rtp file. It is worth noting that the atom name must be unique, and cannot be repeated within the same residue, and it must be designated as a bond.

If you want to introduce new residues into the existing force field so that you can use pdb2gmx for processing.

1. First add the residue name to the /GMX installation path/share/gromacs/top/residuetypes.dat file, and specify its type.

2. Creating rtp file of residues based on the selected force field.

3. Adding the rtp file of the residue to the rtp file of the corresponding molecule type.

4. If you need to use pdb2gmx -ignh to automatically add hydrogen atoms, then you must create a new entry in the hdb file of the relevant molecular type and specify the number of hydrogen atoms to be added.

5. If the introduced residues use new atom types, then these new atom types and their non-bond parameters need to be added to the atomtypes.atp and ffnonbonded.itp files respectively.

6. If the introduced residues contain new bonding interactions, then these new bonding interactions and their parameters need to be added to the ffbonded.itp file.

7. If the introduced residues involve special connection of other residues, you also need to update the specbond.dat file.

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