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pdb2pqr [2012/11/21 09:24]
landon [Computing the charge on a protein]
pdb2pqr [2012/11/21 10:54] (current)
landon [Computing the charge on a protein]
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         * Oftentimes, other molecules crystalize with the protein and are contained in the PDB file. Sometimes this is intentional (i.e to study the interaction between two molecules), And sometimes it is not (i.e. waters, ions, etc.). Also, be aware that multiple copies of the protein may exist in the file (this happens when more than one protein crystalize in the unit cell). These extraneous molecules will need to be removed from the PDB file in advance. This is most easily done by loading the PDB file up in [[VMD]] and then saving a subset of ions to a new PDB file.         * Oftentimes, other molecules crystalize with the protein and are contained in the PDB file. Sometimes this is intentional (i.e to study the interaction between two molecules), And sometimes it is not (i.e. waters, ions, etc.). Also, be aware that multiple copies of the protein may exist in the file (this happens when more than one protein crystalize in the unit cell). These extraneous molecules will need to be removed from the PDB file in advance. This is most easily done by loading the PDB file up in [[VMD]] and then saving a subset of ions to a new PDB file.
           * With a PDB file loaded up in VMD, highlight your molecule in the //VMD Main// window and select //File// -> //Save Coordinates...//​. In the //Save Trajectory//​ dialog box specify the atoms you want saved. You can use all of the atom selection commands which are used in the //Graphical Representations//​ dialog box (i.e. chain A, resid>​100 and resid<​150,​ etc.)           * With a PDB file loaded up in VMD, highlight your molecule in the //VMD Main// window and select //File// -> //Save Coordinates...//​. In the //Save Trajectory//​ dialog box specify the atoms you want saved. You can use all of the atom selection commands which are used in the //Graphical Representations//​ dialog box (i.e. chain A, resid>​100 and resid<​150,​ etc.)
-  * The conversion can be done online here: [[http://​kryptonite.nbcr.net/​pdb2pqr/​|Online PDB2PQR]]. Or locally from here: [[http://​abacus/​pdb2pqr/​|Local PDB2PQR]].+  * With the PDB preparation done, it's time to convert to a PQR file. The conversion can be done online here: [[http://​kryptonite.nbcr.net/​pdb2pqr/​|Online PDB2PQR]]. Or locally from here: [[http://​abacus/​pdb2pqr/​|Local PDB2PQR]].
     * Type in PDB # or upload PDB file     * Type in PDB # or upload PDB file
     * Choose // PARSE // for force field     * Choose // PARSE // for force field
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     * Look at .pqr file header to check for any errors     * Look at .pqr file header to check for any errors
       * PDB2PQR is very picky about what residue codes are used in the PDB files. If an error occurred the offending residues may need to be renamed in the PDB file or a .mol2 file needs to be supplied to PDB2PQR so it knows how to deal with them. Some residues can be built and have .mol2 files generated by [[http://​davapc1.bioch.dundee.ac.uk/​prodrg/​index.html|PRODRG]].       * PDB2PQR is very picky about what residue codes are used in the PDB files. If an error occurred the offending residues may need to be renamed in the PDB file or a .mol2 file needs to be supplied to PDB2PQR so it knows how to deal with them. Some residues can be built and have .mol2 files generated by [[http://​davapc1.bioch.dundee.ac.uk/​prodrg/​index.html|PRODRG]].
 +  * The output PQR file contains the total charge of the molecule in the header. Below that, the partial charge of each atom is listed along with it's coordinates (second column from the left).

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