Can you attach your PDB file so we can see it?
On Mon, Nov 23, 2015 at 7:05 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Hi,
> i apply all the possible ways but it did not resolve.
>
> > From: ayesha_comsian.hotmail.com
> > To: amber.ambermd.org
> > Date: Mon, 23 Nov 2015 15:36:48 +0500
> > Subject: Re: [AMBER] QMMM: ERROR!
> >
> > 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,
> > > >
> > > >
> > > >
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 23 2015 - 04:30:06 PST
