you'll need to look at the part where you assign the parameters. The
minimization shows that the energy starts positive, then the electrostatic
part gets very large and negative, while the vdw does not go up by much.
Prof Case is correct that it is likely because the ho atom type does not
have a vdw radius, but I don't understand why there is not more repulsion
between O42 and O3. What is the distance between those atoms in the
structure where O42 and H8 overlap? What is the distance from H8 to O3? you
need to check these and see if they make sense, and try to debug the
parameter assignments.
On Wed, May 13, 2015 at 9:21 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Prof. Carlos and Prof. Case,
>
> Thanks for the inputs.
>
> I have also carried out vacuum minimization of IP3 itself, with and without
> using SHAKE. But both attempt also itself failed giving the same error, as
> shown below.
>
>
> *****************************************************************************************************************************************
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 357
> | TOTAL SIZE OF NONBOND LIST = 357
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 5.2742E+02 2.7409E+01 1.1716E+02 P4 2
>
> BOND = 8.4877 ANGLE = 22.8180 DIHED =
> 24.0103
> VDWAALS = 8.2413 EEL = -177.5628 HBOND =
> 0.0000
> 1-4 VDW = 6.0891 1-4 EEL = 635.3332 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -2.9898E+05 4.4500E+07 2.2998E+08 O42 3
>
> BOND = 365.9618 ANGLE = 38.8637 DIHED =
> 25.0991
> VDWAALS = 155.9695 EEL = -300177.8643 HBOND =
> 0.0000
> 1-4 VDW = 5.2069 1-4 EEL = 611.1925 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -1.7285E+07 1.4753E+11 7.6244E+11 H8 10
>
> BOND = 365.5569 ANGLE = 38.8517 DIHED =
> 25.0989
> VDWAALS = 155.4699 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1999 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 150 -6.6469E+07 2.1813E+12 1.1273E+13 O42 3
>
> BOND = 365.5656 ANGLE = 38.8519 DIHED =
> 25.0989
> VDWAALS = 155.4807 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1997 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -3.5359E+08 6.1726E+13 3.1900E+14 H8 10
>
> BOND = 365.5635 ANGLE = 38.8519 DIHED =
> 25.0989
> VDWAALS = 155.4780 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 250 -8.9767E+07 3.9783E+12 2.0560E+13 H8 10
>
> BOND = 365.5625 ANGLE = 38.8518 DIHED =
> 25.0989
> VDWAALS = 155.4768 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 -3.3793E+08 5.6377E+13 2.9136E+14 O42 3
>
> BOND = 365.5642 ANGLE = 38.8519 DIHED =
> 25.0989
> VDWAALS = 155.4789 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 350 -8.0637E+07 3.2102E+12 1.6591E+13 H8 10
>
> BOND = 365.5623 ANGLE = 38.8518 DIHED =
> 25.0989
> VDWAALS = 155.4766 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 400 -1.7019E+08 1.4300E+13 7.3903E+13 H8 10
>
> BOND = 365.5631 ANGLE = 38.8518 DIHED =
> 25.0989
> VDWAALS = 155.4776 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 450 -1.4301E+08 1.0097E+13 5.2183E+13 O42 3
>
> BOND = 365.5646 ANGLE = 38.8519 DIHED =
> 25.0989
> VDWAALS = 155.4795 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 -5.6742E+08 1.5895E+14 8.2148E+14 H8 10
>
> BOND = 365.5636 ANGLE = 38.8519 DIHED =
> 25.0989
> VDWAALS = 155.4782 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 5.2061 1-4 EEL = 611.1998 RESTRAINT =
> 0.0000
> Frac coord min, max: -38635069.530564517 38635070.634237535
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
> **************************************************************************************************************
>
> Here also I have seen that the atoms O42 and H8 get overlapped, though they
> attached to different R group in the IP3. The initial structure looks fine.
> I have used the Gaussian output file has the input to antechamber. The
> frcmod file generated with parmchk was empty. Below is the prep file for
> IP3.
>
>
> ************************************************************************************************************
> 0 0 2
>
> This is a remark line
> molecule.res
> IP3 INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
> 4 O41 o M 3 2 1 1.540 111.208 -180.000 -1.263427
> 5 P4 p5 M 4 3 2 1.570 81.355 -114.633 2.124369
> 6 O42 o E 5 4 3 1.550 112.921 96.131 -1.208453
> 7 O43 o E 5 4 3 1.546 112.279 -33.736 -1.188119
> 8 O4 os M 5 4 3 1.741 105.485 -151.933 -0.737826
> 9 C4 c3 M 8 5 4 1.450 126.985 39.454 0.280346
> 10 H4 h1 E 9 8 5 1.093 109.176 43.158 -0.001173
> 11 C3 c3 M 9 8 5 1.563 109.826 -75.183 0.275427
> 12 O3 oh S 11 9 8 1.435 112.517 88.406 -1.112872
> 13 H8 ho E 12 11 9 1.001 103.797 -54.961 0.717472
> 14 H3 h1 E 11 9 8 1.099 104.906 -28.189 -0.072340
> 15 C2 c3 M 11 9 8 1.543 114.613 -143.781 0.942622
> 16 O2 oh S 15 11 9 1.432 114.279 -63.147 -0.935277
> 17 H7 ho E 16 15 11 0.986 108.726 60.380 0.383055
> 18 H2 h1 E 15 11 9 1.097 107.754 -179.450 -0.133582
> 19 C1 c3 M 15 11 9 1.546 106.561 64.895 -0.348903
> 20 O1 os S 19 15 11 1.440 112.618 166.180 -0.624344
> 21 P1 p5 3 20 19 15 1.734 123.642 -135.874 2.056188
> 22 O11 o E 21 20 19 1.559 104.155 -49.935 -1.207060
> 23 O12 o E 21 20 19 1.552 103.289 -169.606 -1.212929
> 24 O13 o E 21 20 19 1.554 107.672 70.804 -1.186606
> 25 H1 h1 E 19 15 11 1.097 105.863 48.080 0.109668
> 26 C6 c3 M 19 15 11 1.558 109.976 -66.865 0.537179
> 27 O6 oh S 26 19 15 1.444 108.780 150.002 -1.087009
> 28 H9 ho E 27 26 19 0.986 106.336 37.928 0.675044
> 29 H6 h1 E 26 19 15 1.094 107.505 -92.490 0.027409
> 30 C5 c3 M 26 19 15 1.590 116.139 23.814 0.210327
> 31 H5 h1 E 30 26 19 1.092 107.887 145.326 0.086686
> 32 O5 os M 30 26 19 1.450 107.622 -96.174 -0.512920
> 33 P5 p5 M 32 30 26 1.801 129.616 -99.468 1.862803
> 34 O52 o E 33 32 30 1.551 101.554 -147.765 -1.171381
> 35 O53 o E 33 32 30 1.545 106.042 -27.462 -1.129296
> 36 O51 o M 33 32 30 1.548 105.881 94.170 -1.155078
>
>
> LOOP
> C5 C4
>
> IMPROPER
>
> DONE
> STOP
>
> **********************************************************************************************************************
>
> Can you suggest me the immediate steps I should take to debug this by
> looking at the prepi file generated with antechamber.
>
> Many thanks
>
> Anu
>
>
> On Wed, May 13, 2015 at 1:53 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Wed, May 13, 2015, Carlos Simmerling wrote:
> >
> > > looking at the energy after 400 steps is difficult to evaluate, but
> since
> > > the energy is very large and negative and the vdw energy is not that
> > high,
> > > I would guess that you have a parameter problem. overlapping atoms
> should
> > > give very high vdw energies. you'll need to look at your parameters and
> > the
> > > antechamber output to see what's going on.
> >
> > To add to Carlos' suggestions: stop the simulation after 400 steps and
> > look at
> > it visually (or use the checkstructure command in cpptraj.) The most
> > likely
> > culprits are hydrogen atoms that have zero vdW radii, and can get too
> close
> > to other atoms (are you using SHAKE?).
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed May 13 2015 - 07:30:03 PDT
