Sorry, I didn't get this important point. Have you tried to run antechamber using your vina output as an input? You could do something like
grep HETATM output.pdbqt | cut -c1-66 > output.pdb and use acpype to prepare the topology, with output.pdb as an input file. https://code.google.com/p/acpype/ This should work fine later to start your md simulations as it should conserve your docked coordinates. Cheers, Gian On 9/17/14 3:56 PM, James Starlight wrote: > all manual and GUI operations are not accepted here! > I'm dealing with the a huge number of protein-ligand complexes (many > many different proteins but only 1 ligand- so the situation is not very > bad !). But what is bad that I need to dock each complex using vina and > make its parametrization by amber > > :) > > James > > 2014-09-17 15:32 GMT+02:00 Gianluca Santoni <gianluca.sant...@ibs.fr > <mailto:gianluca.sant...@ibs.fr>>: > > 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> > > <mailto: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> > > <mailto: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> > > <mailto: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 > <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 > > > > > -- > 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. 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 > > -- 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. 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
