Hi Fernando,
Thanks for trying ACPYPE.
I guess if you're using acpype, you certainly tried with option 'acpype -d
-n -4 …', right? With '-d' you have the debug mode, which prints out all
the commands being executed under the hood. And if you still executing only
the the antechamber command with -nc -4 and sqm is failing, well, then
there's not much acpype can do here.
Alan
On 15 November 2012 08:31, <fmgarcia.cbm.uam.es> wrote:
> Dead David,
>
> 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.
>
> Do you have any suggestion about this?
>
> Thank you.
>
> Be regards,
>
> Fernando
>
>
> On Wed, 14 Nov 2012 12:30:27 -0500, David A Case wrote:
> > On Wed, Nov 14, 2012, Fernando Mart??n Garc??a wrote:
> >> I'm trying to obtain my ligand prep and frcmod files of GTP
> >> following
> >> this tutorial:
> > (Aside: note that there are already GTP parameters in the contributed
> parameter database)
> >> Error: cannot run "/opt/amber12/bin/sqm -O -i sqm.in -o
> >> sqm.out"
> >> of bcc() in charge.c properly, exit
> > You have to look at the sqm.out file to see what the error is. The
> charge
> > depends on how many protons you have in the input file, but -4 is
> probably the
> > most relevant form.
> > ...dac
> > _______________________________________________
> > 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/
> ==============================================
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 15 2012 - 04:00:02 PST
