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.)
>>
>> ....dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> ==============================================
> Fernando Martín García
> Molecular Modelling Group - Lab 312.1
> Molecular Biology Center "Severo Ochoa"
> C/ NICOLáS CABRERA, 1.
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web: http://fertoledo.wordpress.com/
> ==============================================
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 1.
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 Nov 16 2012 - 08:30:02 PST
