I checked the structure as suggested, there are no overlaps or steric
clashes in the input file.
The restraint energies as well as the bond angle energies are large. I
used ambmask utility to make sure I am constraining the right HAP atoms in
the system. Is it possible that large ionic radii (non bonded parameters)
in the file causes issues?
Here is my frcmod file
Bonded parameters and revised vdW parameters for hydroxyapatite
MASS
ca+h 40.08
pap 30.97380
oap1 16.00
oap2 16.00
hop 1.007970
Cl- 35.45
BOND
pap-oap1 430.0 1.570 from HO-OH
oap2-hop 500.0 0.940 from O2-P
ANGLE
oap1-pap-oap1 109.47 125
pap oap1 hop -115.0 50
DIHE
IMPR
NONB
ca+h 3.30 0.130
pap 4.30 0.280
oap1 3.40 0.070
oap2 3.70 0.080
hop 0.0001 0
Cl- 2.513 0.0355910
On 15 August 2016 at 21:39, David A Case <david.case.rutgers.edu> wrote:
> On Mon, Aug 15, 2016, Neha Gandhi wrote:
> >
> > There is some issue with the energies in particular vDW
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 1.9642E+09 4.1580E+04 5.6744E+06 HA 3277
> >
> > BOND = 585136.3558 ANGLE = 319433.4389 DIHED =
> > 2572.6253
> > VDWAALS = ************* EEL = -5610131.6247 HBOND =
> > 0.0000
> > 1-4 VDW = 1839.8371 1-4 EEL = 11004.4573 RESTRAINT =
> > 0.0000
>
> You have two atoms almost on top of one another in your initial structure.
> Use the checkoverlap command in cpptraj to get more information.
> Minimization
> will probably help, but be sure to use a CPU version of sander or pmemd,
> not the GPU version.
>
> Also, the initial values for the bond and angle energies are quite large:
> see what happens to them upon minimization.
>
> >
> >
> > When I visualise the .rst file after minimisation, it seems that the HAP
> > surface is significantly changed as compared to the initial input.
>
> Do you get a very high restraint energy? Check the output, and/or use the
> ambmask utility, to make sure that your restraintmask is affecting the
> atoms you want.
>
> ....dac
>
>
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>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Received on Mon Aug 15 2016 - 22:30:02 PDT
