Hi Fernando,
It's quite possible that you are simply asking too much from AM1/d.
Perhaps it is not made overly clear in the manual, but the default AM1/d
parameters for phosphorous, oxygen, and hydrogen are actually from the SRP
AM1/d-PhoT Hamiltonian, which was parameterized against the "standard"
carbon parameters. There was absolutely no inclusion of nitrogen in that
training set, so there is good reason to expect that N-H bonds are not very
well modeled. If you are curious about what *was* in the training set, I
suggest taking a look at Nam, *et al.* *J Chem Theory Comput*, *2007*, *3*,
486-504.
Maybe it was a little bit self serving of us to set that as the default,
but since our primary interest in having a d-orbital code was to do
phosphoryl transfer, it made the most sense. If you want to use different
parameters, check out the "parameter_file" option and the syntax for
reading in parameters (although this requires a bit of an expert's touch in
my opinion).
I am not at all certain why the salt bridge is stable on its own. Did you
keep using AM1/d in that case? Another rather counterintuitive fact is
that AM1 and AM1/d are not the same and do not give the same answer when
d-orbitals are not present.
Regards,
Brian
On Fri, May 25, 2012 at 6:22 AM, Fernando Martín García <fmgarcia.cbm.uam.es
> wrote:
> Hello,
>
> I'm working with AM1/d, trying to perform the reaction in a ATPase.
> Everything works fine if I only include ATP and catalytic water in QM
> part and also if I add some residues. The problem start when I add a
> salt-brige (E-R) to QM part. In that case, the geometry of QM part
> breaks. The extra point is that if I only include the salt-bridge, QM
> geometry works fine.
>
> Has anybody the any idea where it could be the problem? Has anybody
> experience with AM1/d and ATPases to give some clue?
>
> Thanks.
>
> est regards,
>
> --
> ==============================================
> Fernando Martín García
> Molecular Modelling Group - Lab 312.1
> Molecular Biology Center "Severo Ochoa"
> C/ NICOLáS CABRERA, 5.
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web: http://fertoledo.wordpress.com/
> ==============================================
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
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Received on Fri May 25 2012 - 06:30:03 PDT
