I`m very sorry it had to submit again. because the previous email`s data was wrong.
Data have been adjusted.
Dear all developers and users.
I use Amber11 and Ambertools1.4 based on cygwin. In Ambertools, I have simulated normal mode calculation using NAB. Under the same conditions, I have conducted nmode calculation using MMPBSA.py. When I compared obtained two types of energy, these are not matched.
(1) What reason does not match?
>input file of MMPBSA.py
nmode
&general
verbose=1, keep_files=1,strip_mdcrd=0,
/
&gb
igb=1,
/
&nmode
nmstartframe=1, nmendframe=1, nminterval=1,
maxcyc=10000, drms=0.001, dielc=1.0,
nmode_igb=1, nmode_istrng=0.0,
/
>input file of NAB
molecule mol;
int natm;
float x[ dynamic ], g[ dynamic ], fret;
float dgrad;
int ier;
mol = getpdb( "nmode_nab.pdb" );
readparm( mol, "nmode.prmtop" );
natm = mol.natoms;
allocate x[ 3*natm ]; allocate g[ 3*natm ];
mm_options( "ntpr=10000, gb=1, gbsa=1, surften=0.0072, kappa=0.0, rgbmax=999.0, cut=999.0, diel=C, dielc=1.0, epsext=78.3, temp0=298.15, e_debug=0");
mme_init( mol, NULL, "::ZZZ", x, NULL );
setxyz_from_mol( mol, NULL, x );
printf("\n\n Conj. Gra. Method\n");
dgrad=0.005;
ier = conjgrad(x, 3*natm, fret, mme, dgrad, 1.0, 500);
// Newton-Raphson minimization
mm_options( "ntpr=10000, gb=1, gbsa=1, surften=0.0072, kappa=0.0, rgbmax=999.0, cut=999.0, diel=C, dielc=1.0, epsext=78.3, temp0=298.15, e_debug=0");
dgrad = 3*natm*1E-8;
ier = newton( x, 3*natm, fret, mme, mme2, dgrad, 0.0, 15 );
// get the normal modes
printf("\n\nNMODE Calc\n");
ier = nmode( x, 3*natm, mme2, 0, 0, 0.0, 0.0, 0);
PDB file was made by LMOD conformational search.
Topology file and coordinate file were created by below..
source leaprc.GLYCAM_06
set default write14scale on
a = loadpdb *.pdb
saveamberparm a *.prmtop *.inpcrd
quit
> PDB file
REMARK 1 PDB file generated by ptraj (set 1)
ATOM 1 HO1 ROH 1 -1.949 4.394 -3.811 0.00 0.00
ATOM 2 O1 ROH 1 -1.331 3.672 -4.036 0.00 0.00
ATOM 3 C1 4GB 2 -1.618 2.568 -3.165 0.00 0.00
ATOM 4 H1 4GB 2 -2.633 2.216 -3.361 0.00 0.00
ATOM 5 O5 4GB 2 -1.542 3.048 -1.777 0.00 0.00
ATOM 6 C5 4GB 2 -1.763 2.020 -0.725 0.00 0.00
ATOM 7 H5 4GB 2 -2.759 1.596 -0.868 0.00 0.00
ATOM 8 C6 4GB 2 -1.734 2.704 0.655 0.00 0.00
ATOM 9 H61 4GB 2 -2.547 3.428 0.722 0.00 0.00
ATOM 10 H62 4GB 2 -1.876 1.969 1.447 0.00 0.00
ATOM 11 O6 4GB 2 -0.477 3.390 0.861 0.00 0.00
ATOM 12 H6O 4GB 2 -0.374 4.049 0.147 0.00 0.00
ATOM 13 C4 4GB 2 -0.724 0.895 -0.885 0.00 0.00
ATOM 14 H4 4GB 2 0.271 1.293 -0.672 0.00 0.00
ATOM 15 C3 4GB 2 -0.739 0.322 -2.317 0.00 0.00
ATOM 16 H3 4GB 2 -1.686 -0.202 -2.466 0.00 0.00
ATOM 17 O3 4GB 2 0.347 -0.639 -2.461 0.00 0.00
ATOM 18 H3O 4GB 2 0.389 -1.172 -1.642 0.00 0.00
ATOM 19 C2 4GB 2 -0.594 1.420 -3.397 0.00 0.00
ATOM 20 H2 4GB 2 0.418 1.830 -3.358 0.00 0.00
ATOM 21 O2 4GB 2 -0.810 0.814 -4.709 0.00 0.00
ATOM 22 H2O 4GB 2 -0.208 0.046 -4.776 0.00 0.00
ATOM 23 O4 4GB 2 -1.060 -0.197 0.065 0.00 0.00
ATOM 24 C1 0GB 3 -0.008 -0.517 1.041 0.00 0.00
ATOM 25 H1 0GB 3 0.342 0.406 1.506 0.00 0.00
ATOM 26 O5 0GB 3 1.115 -1.182 0.360 0.00 0.00
ATOM 27 C5 0GB 3 2.260 -1.543 1.241 0.00 0.00
ATOM 28 H5 0GB 3 2.641 -0.628 1.700 0.00 0.00
ATOM 29 C6 0GB 3 3.370 -2.162 0.372 0.00 0.00
ATOM 30 H61 0GB 3 4.241 -2.403 0.982 0.00 0.00
ATOM 31 H62 0GB 3 3.013 -3.083 -0.093 0.00 0.00
ATOM 32 O6 0GB 3 3.766 -1.232 -0.662 0.00 0.00
ATOM 33 H6O 0GB 3 2.959 -0.973 -1.149 0.00 0.00
ATOM 34 C4 0GB 3 1.759 -2.496 2.348 0.00 0.00
ATOM 35 H4 0GB 3 1.481 -3.450 1.896 0.00 0.00
ATOM 36 O4 0GB 3 2.836 -2.722 3.300 0.00 0.00
ATOM 37 H4O 0GB 3 2.474 -3.254 4.038 0.00 0.00
ATOM 38 C3 0GB 3 0.538 -1.907 3.096 0.00 0.00
ATOM 39 H3 0GB 3 0.859 -1.039 3.677 0.00 0.00
ATOM 40 O3 0GB 3 0.013 -2.914 4.013 0.00 0.00
ATOM 41 H3O 0GB 3 -0.801 -2.550 4.416 0.00 0.00
ATOM 42 C2 0GB 3 -0.578 -1.469 2.120 0.00 0.00
ATOM 43 H2 0GB 3 -0.997 -2.350 1.628 0.00 0.00
ATOM 44 O2 0GB 3 -1.639 -0.796 2.862 0.00 0.00
ATOM 45 H2O 0GB 3 -2.352 -0.572 2.232 0.00 0.00
>result(MMPBSA.py)
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 98.67 16.90 -0.48 139.08 0.00 -56.82 8.39e-04
Energy = 9.8671303528e+01
RMS gradient = 8.3915466343e-04
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 342.296
Principal moments of inertia in amu-A**2:
1254.94 3540.24 4195.11
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.019 0.007 0.006
Zero-point vibrational energy: 229.164
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 343.707 94.671 171.069
translational: 0.888 2.979 43.357
rotational: 0.888 2.979 35.071
vibrational: 243.259 88.714 92.642
ff energy: 98.671
1 -0.233
2 -0.000
3 0.000
4 0.000
5 0.030
6 0.135
7 15.895 0.592 1.985 7.084
8 28.399 0.593 1.983 5.933
9 33.535 0.593 1.982 5.603
10 54.692 0.596 1.974 4.636
11 74.431 0.598 1.965 4.028
12 81.647 0.600 1.960 3.847
>result(NAB)
NMODE Calc
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 98.67 16.89 -0.48 139.08 0.00 -56.82 1.66e-02
Energy = 9.8673201693e+01
RMS gradient = 1.6578972407e-02
dysev time = 0.00 seconds
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 342.296
Principal moments of inertia in amu-A**2:
1254.93 3540.35 4195.41
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.019 0.007 0.006
found 3 imaginary frequencies
Zero-point vibrational energy: 229.041
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 341.923 88.733 152.499
translational: 0.888 2.979 43.357
rotational: 0.888 2.979 35.071
vibrational: 241.474 82.775 74.072
ff energy: 98.673
1 -2.453
2 -1.584
3 -1.359
4 -0.000
5 0.000
6 0.000
7 15.668
8 28.271
9 33.396
10 54.572 0.596 1.974 4.640
11 74.358 0.598 1.965 4.030
12 81.540 0.600 1.960 3.849
(2) And what is the reason for the different Default of mm_options of MMPBSA.py and NAB? Especially why the default value of dielectric constant(dielc)is 4.0 and how to control rgbmaxin MMPBSA.py?
Thank you.
Lee
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Received on Thu Sep 20 2012 - 07:30:03 PDT
