.. raw:: html 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). For details please refer to `CAMPARI documentation `_. The sequence file can be extracted from the ``SEQRES`` of the pdb using the script ``convert_SEQRES_toseq.sh`` provided by CAMPARI. Before starting the preparation with CAMPARI be sure to have run: .. code-block:: bash cvs update If you specify in the key file the following keyword .. code-block:: bash FMCSC_SYBYLLJMAP ljmap_for_abs4.2_charmm36.prm CAMPARI will write structural mol2 files with the ``ALT_TYPE_SET`` specification as required by SEED. Be sure also to use the correct CHARMM parameters: .. code-block:: bash PARAMETERS campariv3/params/abs4.2_charmm36.prm The written mol2 files will contain the CAMPARI biotypes which will have to be remapped to the correct CHARMM atom types by using: .. code-block:: bash bash convert_CAMP_BIO_to_CGENFF.sh CAMP_BIO_to_CGENFF.map MOL2FILE > OUTPUTFILE 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``) is carried out to remove any major steric clash. The relaxed output (pdb with suffix ``_RELAXED.pdb``) can be used as structural input for the minimization, which is performed in internal coordinates by ``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 ones (the ones we would like to freeze) from a CAMPARI log file (keyword ``TMDREPORT`` enabled), with a command like the following: .. code-block:: bash 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``.