Dear Jianhui Tian,
Looking at this structure took 2 sec to be loaded in vmd, and by
simply looking at this ATP analog:
The problem you encounter was discussed several times & the answer is known:
- problem of convergence? try a more robust program...
- can you get an optimized structure? if yes, its conformation will be
all, but representative...
I would not optimize this type of whole molecule with multiple charge
values. Instead I would use the building block approach; i.e. R.E.D.
Server & R.E.D. IV and not antechamber in this type of work...
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
regards, Francois
> Sorry to bother and take your time again.
>
> The no convergence happens during the sqm calculation for charge.
> Is it doable/reasonable to get the topology like this:
> 1. calculate the topology for the AMP PNP with -2 charge (this charge can
> converge)
> 2. get the charges using another way
> 3. fix the charges in the final topology file
> The assumption I have here is the bonded and vdw parameter will not be
> affected by the net charge of the ligand.
>
> Otherwise, I do not know how to run the antechamber in a
> broke-up/step-by-step way.
> On Mon, Sep 16, 2013 at 10:13 AM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Fri, Sep 13, 2013, Jianhui Tian wrote:
>> >
>> > Please find in the attachment the PDB of AMPPNP I used. Thanks a lot for
>> > your time and your kind help.
>>
>> This is a problem that requires more time than I have had so far. It may
>> be a
>> problem with the initial geometry. What I've found so far is that
>> Gaussian09
>> also fails with this input, and that PM6 seems OK, and can optimize the
>> geometry fine. I've not yet had time to investigate other options; you
>> might
>> try geometry optimization at the PM6 level, then try using that for AM1
>> calculations.
>>
>> Of course, in general, using gas-phase calculations for a -4 anion is a
>> stretch. You might consider adding a proton and looking at the -3 state,
>> since the pKa of ATP is around neutral pH.
>>
>> ...dac
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Received on Tue Sep 17 2013 - 00:30:03 PDT
