The problem is that during processing of any ligand.mol2 files consisted of
full sets of hydrogen I've obtained an error from antechamber
antechamber -i Benzyl-acetate-OK.mol2 -fi mol2 -o ligand.mol2 -fo mol2 -c
bcc
Total number of electrons: 80; net charge: 0
Running: /+SOFTWARE/amber12/bin/sqm -O -i sqm.in -o sqm.out
/+SOFTWARE/amber12/bin/sqm: symbol lookup error:
/+SOFTWARE/amber12/bin/sqm: undefined symbol: __svml_exp4_mask
Error: cannot run "/+SOFTWARE/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit
! this happens only when I run antechamber from bash but not from csh so it
resemble some bug.
James
2014-09-16 13:55 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
> It is not quite clear what you are asking for, you say "hybridization"
> in the context of some "cyclic" groups. Maybe you mean more
> specifically the protonation state/tautomerism. In this case, my
> recommendation would to read e.g. DOI:10.1007/s10822-010-9329-5 (one
> chemoinformatician's point of view) and understand that this may be a
> problem much more complicated than just throwing a file at an
> algorithm. Chemists tend to be "sceptical" about such approaches. If
> that is not the problem the software is still reliant on "reasonable"
> input structures (you don't say how you got to those).
>
> Cheers,
> Hannes.
>
>
> On Tue, 16 Sep 2014 15:14:59 +0400
> James Starlight <jmsstarlight.gmail.com> wrote:
>
> > Dear Amber users!
> >
> > Using antechamber I need to parametrize broad set of the ligands,
> > dock it with the receptors and proceed complexes for further md run.
> > The problem on the first step: is due to all of those ligands are
> > consisted of several bulk cyclic group so it's hard to determine
> > hybridization of each C atom and compute precice number of hydrogens
> > (I've tried to do it by chimera pymol and babel taking ligands
> > stripped from any hydrogens as the input structures). Could someone
> > suggest me some software(or alternatively combination of commands for
> > above listed ones) to solve this issue?
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Sep 16 2014 - 08:00:05 PDT
