Dear David and AMBER
The output of sqm shows following
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2226E+07 DeltaE = -0.1907E+02 DeltaP = 0.2175E+00
QMMM: Smallest DeltaE = -0.3600E-06 DeltaP = 0.1452E-04 Step = 2
As suggested in link:
http://archive.ambermd.org/201808/0051.html
I did minimization of my structure by avogadro before puting in to
antechamber.
Here is the pdb attached
Please suggest me is there anything wrong with input structure?
thank you
On Tue, Jun 25, 2019 at 2:59 AM David Case <david.case.rutgers.edu> wrote:
> On Mon, Jun 24, 2019, Sadaf Rani wrote:
> >
> >protein = loadPdb "Combined_nolig.pdb"
> >complex = combine {protein ligA ligB}
> >protein = createUnit Combined_nolig.pdb
>
> This isn't doing what you probably think: "createUnit" creates a new and
> empty
> unit with the name protein. This overwrites (I think--I hardly ever use
> this
> command) your earlier definition of "protein".
>
> >setBox protein "vdw"
>
> This is not needed, since the next command sets the box anyway.
>
> >solvateBox protein TIP3PBOX 14.0 iso
> >addIonsRand complex Na+ 0
>
> Is this what you want? You used "solvateBox" on "protein", but
> "addIonsRand"
> on "complex".
>
> Approach I recommend: avoid commands like combine and createUnit. Prepare
> by
> hand a single pdb file with everything you want in it, then use a single
> loadPdb command to create the unit.
>
> >Running: /home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o sqm.out
> >/home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> >Cannot properly run "/home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o
> >sqm.out".
>
> The intention is for you to look in the sqm.out file to see what the
> problem
> might be. (Scott: can this get added to the message?)
>
> Note that parameterizing anions (and especially phosphates) are difficult,
> and
> often require hand-preparation.
>
> ....dac
>
>
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Received on Tue Jun 25 2019 - 08:00:02 PDT
