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:

cvs update

If you specify in the key file the following keyword

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:

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:

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:

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.