Re: [AMBER] Antechamber ligand parametrization

From: James Starlight <>
Date: Wed, 17 Sep 2014 11:45:14 +0200


thank you very much for the suggestions- the problem was exactly in those

New question about preparation of protein-ligand complexes for md

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 assosiated 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 . Will it possible using
amber's ligand.lib to restore full-atomic structure of the ligand based on
its (no H) coordinates obtained from docking ? Are there some alternative
solutions (e.g to use pdb2pqr with the receptor_ligand.pdb to make
preparation of the coordinates for amber param-sets)?

Thanks for help,


2014-09-16 21:53 GMT+02:00 David A Case <>:

> On Tue, Sep 16, 2014, James Starlight wrote:
> > /+SOFTWARE/amber12/bin/sqm: symbol lookup error:
> > /+SOFTWARE/amber12/bin/sqm: undefined symbol: __svml_exp4_mask
> >
> > ! this happens only when I run antechamber from bash but not from csh so
> it
> > resemble some bug.
> This is not an antechamber or Amber problem. Almost certainly, your
> environment in bash is not the same as your environment in csh. Check
> especially the LD_LIBRARY_PATH environment variable. It looks like you are
> using the Intel compilers, but that your bash environment has not properly
> set
> up the corresponding environemnt variables.
> As a sanity check, make sure you can run the test cases from your bash
> shell.
> ...dac
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Received on Wed Sep 17 2014 - 03:00:02 PDT
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