Protein preparation with CAMPARI

With the latest implemented features it is now straightforward to use CAMPARI to directly generate a receptor mol2 file for SEED. As CAMPARI’s pdb parser is fairly robust, in the vast majority of the cases it will be able to read a raw pdb without the need of any preprocessing.

The input files required by CAMPARI to describe the receptor are a sequence file listing all the residues in the system and a pdb or another structural file to read the atom coordinates (the atoms for which no coordinates are provided will be rebuilt by CAMPARI). Additionally CAMPARI only requires a key file with a list of keywords specifying the calculation to run. We provide some key file templates to perform a standard protein preparation protocol for docking. For details please refer to CAMPARI v4 documentation.

The sequence file can be extracted from the SEQRES of the pdb using the script provided in the CAMPARI tool directoty.

Before starting the preparation with CAMPARI be sure to be running version 4. Once the key-file is specified, CAMPARI can be run as easy as:

campari -k keyfile.key >& log

By default CAMPARI will write as structural output both a pdb and a mol2 file with the ALT_TYPE_SET specification as required by SEED.

We recommend using CHARMM parameters for docking with SEED. Using AMBER/GAFF force field is still experimental, but can be done (see Gaff preparation (WORK IN PROGRESS)). CHARMM parameters can be specified in the key-file with the following keyword:

PARAMETERS  <CAMPARI_PATH>/params/abs4.2_charmm36.prm

The output mol2 files will contain CHARMM partial charges (in the charge column) and the CAMPARI biotypes (in the ALT_TYPE_SET line), which needs to be mapped to the corresponding CHARMM atom types by running:


A protein receptor can be prepared with CAMPARI using the two keyfiles tmd_build.template.key and cons_mini_abs_internal.template.key (make sure to correct filenames and paths).

tmd_build.template.key rebuilds the system starting from the provided pdb. Missing residues are added and missing sidechains are build in random conformations. After that a specific relaxation protocol (refer to keyword TMD_RELAX in CAMPARI documentation) is carried out to remove any major steric clashes.

The mol2 output of the run (suffix _RELAXED.mol2 or _END.mol2) is almost ready to be used in SEED (only the remapping of CHARMM atom types is needed). Note that the RELAXED files contains the system coordinates after the relaxation, whereas the END files are the final snapshots of the simulation, in case for example additional molecular dynamics or Monte Carlo is run after relaxation.

We recommend to additionally run a short minimization on the relaxed output (pdb with suffix _RELAXED.pdb). Minimization can be performed in internal coordinates with cons_mini_abs_internal.template.key. We recommend the use of a freeze file (keyword FRZFILE, using mode A) to allow only side-chain terminal dihedrals (those ending with a hydrogen) to move during minimization. This can be accomplished for example by extracting the indices of the non-terminal dihedrals (the ones we would like to freeze) from a CAMPARI log file (keyword TMDREPORT enabled), with a command like the following:

sed -n '/Summary of Rotation/,/End of Summary of Rotation/p' log | sed '/Mol.  #/,/Atom/d' | tail -n +2 | head -n -1 | awk '$3 > 10 {print $1}'

If the system is made up by multiple chains or molecules, make sure to include also constraints for rigid body translations and rotations in the FRZFILE.

For the equivalent target preparation protocol for AMBER/GAFF, refer to Writing a SEED-compatible receptor with AMBER parameters.