AMBER Archive (2009)
Subject: Re: [AMBER] using sqm from AmberTools 1.3
From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 29 2009 - 14:10:56 CST
Thank you all for the reply.
Watson, I will reply you later.
I have more to add here.
First I contacted my office mates at EBI PDBe asking more about GNP in 1e0A
because clearly there's misleading information in our data.
Dear Case, where did you see -4 for the ligand? Now it would make sense in
face what I know.
Apparently, I am trying antechamber in GNP (45 atoms, from 1e0a) using an
information from PDBe Ligand DB that this ligand should have charge 0, and
now I can understand that this charge 0 came from the ligand with 49 atoms.
So, clearly, the information at PDBe Ligand DB is driving me wrong here and
causing all these messes I am reporting here.
Thanks a lot you guys. I will investigate what would be the net charge for
GNP 45 (gasteiger suggest -2 and testing with that all goes fine, but still,
where did you find -4 dear Case?)
On Tue, Dec 29, 2009 at 19:36, case <case_at_biomaps.rutgers.edu> wrote:
> On Tue, Dec 29, 2009, Alan wrote:
> > First, the molecule is the ligand GNP in 1E0A from PDB:
> > http://www.pdb.org/pdb/explore/explore.do?structureId=1E0A
> The ligand there has a net charge of -4: is that what you used?
> This is not a crazy charge assignment, although I would expect the terminal
> phosphate group to have an extra proton attached at pH 5.5....
> > The problem is that in the complex 1E0A (done in pH 5.5), GNP has only 13
> > and not 17 H as shown in formula or in the ligand links above.
> The "ligand links" show a (hypothetical) neutral ligand, that would only
> such a protonation state at extremely low pH.
> > So, trying to summarise. GNP_1E0AS0 failed, even after 10 hours. From
> > sqm.out log file, some excerpts:
> > QMMM: WARNING!
> > QMMM: Unable to achieve self consistency to the tolerances specified
> > QMMM: No convergence in SCF after 1000 steps.
> Ross (and other developers): we need to issue a bug fix to make this a
> error, certainly for stand-alone sqm. Do you agree?
> Further exploration: if I use the ligand from the 1E0A file with mopac
> Amber10) it works OK (with a charge of -4).
> If I use sqm, however, I get the convergence failure noted above. However,
> if I take the optimized structure from the mopac run, and feed it to sqm,
> things work fine.
> For developers (Ross, Andreas): I'm including an sqm_bad.in (which is the
> original geometry), and an sqm_good.in (which has the mopac-optimized
> geometry). The geometries are not that much different -- some changes in
> torsional angles, but nothing drastic. So: is there some parameter that
> be tweaked to improve SCF convergence for the "bad" case? Something else
> that is inhibiting sqm for this molecule?
> ...good luck....dac
> AMBER mailing list
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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