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 <[email protected]>:
> 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 <[email protected]>:
>
>> 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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