Dear Fernando,
You might be interested in the 'F-90' project in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/projects/F-90/ &
http://q4md-forcefieldtools.org/REDDB/projects/F-91/
You will find GTP (with two protonation states) and far more i.e. more
than 200 biochimical cofactors in this project...
The 'building block' approach was followed; this allows rigorously
controlling the conformation of the building blocks that compose the
whole molecule(s); this takes a particular importance for multiply
charged molecules, where the geometry of the whole molecule (i.e. GTP
in your case) obtained after geometry optimization is unlikely to be
representative...
regards, Francois
> Sorry again, but I have realized of one problem. If I use gtp without
> protons, acpype works fine (antechamber runs with the mol2 file). But
> if I add protons to the base and ring (as it is how it is as ligand in
> a protein), it is when problems start again (same I described before).
>
> So I don't know really what's the problem with the protons.
>
> Fernando
>
> On Fri, 16 Nov 2012 13:09:59 +0100, Fernando Martín García wrote:
>> Dear David,
>>
>> You were right. I've changed my initial structure of GTP (the other one
>> came from a dynamic) and now antechamber works fine, and acpype too.
>>
>> Thanks for your answer and time
>>
>> Best regards,
>>
>> Fernando
>>
>> On Thu, 15 Nov 2012 08:06:59 -0500, David A Case wrote:
>>> On Thu, Nov 15, 2012, fmgarcia.cbm.uam.es wrote:
>>>>
>>>> Thank you for your answer. You are right -4 is the most relevant
>>>> form. I
>>>> tried it with -nc -4, but problem persists.
>>>>
>>>> sqm.out error is the next:
>>>>
>>>> QMMM: ERROR!
>>>> QMMM: Unable to achieve self consistency to the tolerances
>>>> specified
>>>> QMMM: No convergence in SCF after 1000 steps.
>>>> QMMM: E = -0.1228E+07 DeltaE = 0.6632E+02 DeltaP = 0.1034E+00
>>>> QMMM:
>>>> Smallest DeltaE = -0.5975E-01 DeltaP = 0.3941E+00 Step = 765
>>>>
>>>>
>>>> According to the parameters, yes, you are right that there is a
>>>> data set
>>>> where you can find GTP prep. But the problem is based on I want to
>>>> convert this parameter to Gromacs topology file using acpype
>>>> program.
>>>> But it fails in this step.
>>>
>>> Please see Note 6 in section 4.2 of the AmberTools12 manual. But
>>> also make
>>> sure that you have a good initial geometry, and that -4 is the
>>> correct charge
>>> for the geometry you are using (i.e. that there are no hydrogen atoms
>>> on the
>>> phosphate groups.)
nfo/amber
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Received on Fri Nov 16 2012 - 09:00:02 PST
