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>:
> 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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