Hi James, what usually worked for me was simply to do it manually, in editing mode with pymol. Consider that you will perform an energy minimization after, so a few 1/10 of angstroms of difference in your initial model are not a big deal, in my opinion.
Cheers, Gian On 9/17/14 3:17 PM, James Starlight wrote: > Hi Fotis, > > thank you very much for the suggestion! > > Indeed I have not had such problem with the preparation structure for > NAMD but in case of amber its really exist (the structure of the ligand > provided in the complex with the receptor.pdb must be EXACTLY the same > as it was previously parametrized using some amber program called > antechamber). > So I will be interesting in two options > 1) to find some shell utility for superimposition of the 2 ligands in > one-style command (because here I'm dealing with some script and I need > to do it in loop many times) > or (which is better!) > > 2) use pdb2pqr software (because I'm using it in the part of this script > to process complex and to add hydrogens to ligand as well)- here I > noticed that ligand should be provided as the separate .mol2 file (not > pdb)- which is a bit not comfortable for me (because I obained all > docking poses from VINA as the pdb). I guess I should here to put ligand > from complex, to convert it to mol2 and proceed 2 files (receptor and > ligand) to the pdb2pqr. But may be the better solution is exist? > > James > > > > 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas <fotis.baltou...@gmail.com > <mailto:fotis.baltou...@gmail.com>>: > > Hello James, > You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or > the pair_fit command to superimpose small molecules. It's not as > straightforward as protein super/align, since you have to define the > atom pairs that will be superimposed, but it's fairly easy. After > that, just make a selection of your receptor and your new ligand and > save it as a molecule. > > However, I don't think you really have a problem here. Since the > only issue you mention is the lack of hydrogen atoms, couldn't you > just reintroduce them through some function in the AmberTools? I > have no experience with Amber parameterization tools but, if they're > even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they > can add hydrogen atoms for you easily. > Another option would be to create a PQR file, either through PDB2PQR > (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools > GUI in PyMOL. Part of the PQR creation includes adding hydrogen > atoms, and you can use AMBER parameters both for proteins and for > ligands (mol2 format). Your result would be the structure of your > complex, with hydrogens, in the AMBER format. > > Hope I helped, > Fotis Baltoumas > > 2014-09-17 13:01 GMT+03:00 James Starlight <jmsstarli...@gmail.com > <mailto:jmsstarli...@gmail.com>>: > > Dear Pymol users, > > I've decide to make a copy of this topic from the amber mail > list because this problem could be solves by ones of the methods > implemented in Pymol. > > Here I'm facing with the problem of the preparation of > protein-ligand complexes for amber md simulation: > Following amber's tutorial I've made parametrization of the > ligand using antechamber obtaining ligand.frcmod and ligand.lib > files consisted of the parameters for my ligand and its > coordinates in mol2 associated with those topologies. Now I'd > like to dock this ligand to the active site of the receptor > using autodock vina and make further tleap processing of > complex.pdb produced by autodock to obtain all input data for > simulation. Here some problems: because (superimposed to the > receptor cavity) ligand.pdb produced by autodock have been > stripped from all hydrogen’s so its coordinates not equal to > initial ligand.mol2 . How do you think will it possible to use > some method of the ligand superimposition to superimpose initial > ligand.mol2 (with correct corrdinates) agains docking pose > produced by vina and use superimposed ligand.mol2 for the > preparation of my complex? > > Thanks for help, > > James > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > > > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _________________________________________________________ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. 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