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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Received on Wed May 13 2015 - 06:30:08 PDT
