A collection of small utilities in Python that I have found useful when working with Amber. The utilities have been tested with Amber14 and AmberTools15.
13th November 2016: Added two new tools: AutoSub, which automates the use of Modeller to make substitutions, and RenameChain, which changes the ID of a chain in a PDB file. Expanded the documentation, and provided example commands to effect a substitution.
Tools for Structure Preparation
Tools for Trajectory Analysis
Tools for MMPBSA.py Analysis
All tools require Python 2.7. Other dependencies are given under the usage instructions for specific tools. The PDB-oriented tools have been written to conform to version 3.3 of the PDB File Format and only use basic features. They have been tested on a number of structures, but may have issues with some PDB files, particularly older ones as they were not so rigorously format checked. If you run into problems I will be happy to help - or even happier to receive push requests with fixes!
Some residue names in the PDB file need to be changed before simulation - for example HIS residues need to be renamed to HID, HIE or HIP to reflect the correct protonation state, and CYS residues participating in disulphide bonds need to be changed to CYX. ConvertRes takes a control file listing residue names to be changed, and makes the appropriate changes to the PDB file. This saves time and makes it easy to see later which changes have been made.
MolProbity includes a supervised tool for determining histidine protonation. The output is a correctly protonated PDB file. ResToAmber analyses such a file, and creates a control file for ConvertRes that will rename the HIS records to reflect appropriate Amber residue names. It also looks for SSBOND records, and, if found, generates control records to convert the corresponding CYS residues to CYX.
LEaP uses PDB CONECT records to determine the atomic linkage of disuplhide bonds, however these records are sometimes not included in PDB files. If SSBOND records are present, MakeConects will create CONECT records from the SSBONDS. Changes to the PDB file can disrupt the numbering of atoms and it is a good idea to ensure that atom numbering is clean before running MakeConects: this can be done by running RenumberAtoms. RenameChain is a simple tool that can be used to change the chain ID in a PDB file, which can sometimes be convenient, for example if the PDB file contains multiple chains with the same ID.
LEaP refers to residues using numbers that start at the first residue number in the PDB file and increment sequentially through the PDB file without reference to chains, insertions or omitted residue numbers. AmberNum will create a reference table that makes it easy look up the corresponding PDB's chain numbering.
It may be necessary to insert residues which were not reported in the structure file, or it may be desired to effect substitutions. Where Modeller is used, the Modeller output will consist of a single chain, with residues numbered sequentially from 1. Any Amber-specific residue names will be reverted to standard, e.g. HIE to HIS etc. AutoSub is a script that will manage the modelling of substitutions, insertions and deletions with Modeller. NumberRes will create from Modeller output a file that includes a chain identifier and, if necessary, a different starting residue number. RelabelChains will create a file that matches the chains and numbering in the original PDB file, and will reproduce the Amber residue names used in that file. ReplaceRes will replace a given range of residues with a replacement set. Typical usage of these tools is explained here.
ExtractResidues script to extract a specified span of residues from a pdb file
Amber trajectory snapshots saved by cpptraj in PDB format have residue numbers ascending from 1 and do not contain chain ids. RelabelChains will restore residue numbers and chain IDs using the initial PDB file as a reference. Solvent molecules at the end of the trajectory file are removed.
These tools assist with the assessment of convergence of MM/GBSA and MM/PBSA energy calculations, and provide graphical summaries of pairwise energy contributions. Where there are multiple identical receptors in the structure, the tools can accumulate results obtained from each ligand against its cognate.
ExtractMMPBSATotals extracts frame-by-frame delta G values using the Python API to MMPBSA.py. Where such files have been collected for multiple receptor/ligand pairs, they can be accumulated by MergeFiles which interleaves the totals from each file in order to preserve correlation.
CalcBounds determines the mean and 95% bootstrapped confidence limits for delta G using the energy total file, and creates charts showing the trend over successive accumulated values and the distribution of the frame-by-frame totals:
PairwiseDecompTable creates a table of delta-G from one or more pairwise energy decompositions. Delta-G values are averaged across the files.
ConsolidateHbonds creates a list of observed h-bonds from one or more files. The resulting list consolidates the count of frames in which an h-bond is observed between atoms in a pair of residues.
DrawInteractions uses the output from PairwiseDecompTable and ConsolidateHbonds to draw an interaction diagram similar to the one below.
CreateInteractionControl creates a control csv for DrawInteractions from the hbonds file generated by ExtractMMPBSATotals.py and the FINAL_DECOMP_MMPBSA_table.csv.
ExtractFramesHighLow Creates cpptraj input files to extract high and low energy frames.