thank u very much again!
the problem is that the vina output is also stripped from the hydrogen ( i
don’t know why because I've made each ligand including hydrogens from the
initial.pdb where they were)
pythonsh ${tools}/prepare_ligand4.py -v -l ${mol2} -o
${ligands_out}/${filenamenoextention_lig}/${filenamenoextention_lig}.pdbqt
-A hydrogens_bonds
so antechamber will also send me error dealing with that stripped files :)
will the acpype available as some software not web server?
James
2014-09-17 16:27 GMT+02:00 Gianluca Santoni <gianluca.sant...@ibs.fr>:
> 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
>> >
>> >
>> ------------------------------------------------------------
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>>
>> --
>> 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
>>
>> ------------------------------------------------------------
>> ------------------
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>> Manually upgrade your production database.
>> When you want reliability, choose Perforce
>> Perforce version control. Predictably reliable.
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>>
>
> --
> 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
>
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