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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--
==============================================
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 - 04:30:02 PST
