i put -ek flag to the below command and it generates sqm.in , sqm.out and mol2 file
antechamber -ek tight_p_conv=0,scfconv=1.d-8,qmcharge=0, -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
But..
it did not show these values in the sqm.in file
qm_theory='AM1', grms_tol=0.0002,
and when i test the parameters through parmchk command
parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
the frcmod shows no angles the results of my frcmod file are:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
c3-n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c -c3-n -c3 1.1 180.0 2.0 General improper torsional angle (1 general atom type)
NONBON
how can i generate angles ? i think it is due to missing value of (qm_theory='AM1', grms_tol=0.0002)
> From: ross.rosswalker.co.uk
> Date: Sun, 22 Nov 2015 21:42:20 -0800
> To: amber.ambermd.org
> Subject: Re: [AMBER] QMMM: ERROR!
>
> Hi Ayesha,
>
> It looks like the minimizer got very close. Sometimes it just doesn't quite make it to the tolerances needed.
>
> You can try mimizing things separately with sqm (outside of antechamber) with scfconv=1.d-8. Then take the final structure from that and use it for your input to antechamber.
>
> Alternatively update to AmberTools15 which has loosened the default antechamber SQM convergence criteria slightly and in your case the SCF should then converge.
>
> All the best
> Ross
>
> > On Nov 22, 2015, at 21:32, Ayesha Kanwal <ayesha_comsian.hotmail.com> wrote:
> >
> > there is an error occur during sqm.out and after that mol2 files could not generated.
> > antechamber -i sustiva_new.pdb -fi pdb -o
> > sustiva.mol2 -fo mol2 -c bcc -s 2
> > the following error occured during this process
> > Error: cannot run "/home/comsats/Desktop/Softwares/amber14//bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> > and the sqm.out is generating the following error
> >
> > RESULTS
> > --------------------------------------------------------------------------------
> >
> >
> > QMMM: ERROR!
> > QMMM: Unable to achieve self consistency to the tolerances specified
> > QMMM: No convergence in SCF after 1000 steps.
> > QMMM: E = -0.3142E+07 DeltaE = -0.2242E-09 DeltaP = 0.4663E-13
> > QMMM: Smallest DeltaE = 0.1869E-09 DeltaP = 0.2397E-06 Step = 3
> >
> > how can i fix this problem ?
> > my sqm.in have these values
> >
> > Run semi-empirical minimization
> > &qmmm
> > qm_theory='AM1', grms_tol=0.0002,
> > tight_p_conv=1, scfconv=1.d-10, qmcharge=0,
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Nov 23 2015 - 03:00:02 PST
