Hi Brian,
Thanks for your answer. When I include only the salt bridge, I'm using
AM1/d too. I have to say that if I include a lysine in the system (next
to ATP), system works fine, but maybe the problem is with the presence
of E in front of R. I have only experience with PM3 and I would have
liked to reproduce my PM3-QM system with AM1/d. By the way, I'm going to
check the article.
Thanks for your answer again,
Fernando
On Fri, 25 May 2012 09:02:46 -0400, Brian Radak wrote:
> 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
> radak004.umn.edu :
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> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> address.
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--
==============================================
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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Received on Fri May 25 2012 - 07:30:04 PDT
