See my last reply, which all still applies (minus the comment about
identical results). The fact that your vibrational entropy is very similar
to MMPBSA.py, I'd say that's expected based on the reasons I gave.
HTH,
Jason
On Thu, Sep 20, 2012 at 10:13 AM, Sangmin Lee <dadu0413.yonsei.ac.kr> wrote:
>
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 20 2012 - 08:00:03 PDT
