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>:
> 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. 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
>
------------------------------------------------------------------------------
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
