Dear David,
> It's not clear exactly what program you tried to compile and execute.
> I've attached my version (bench_nm.nab), along with the output from
> "./a.out gcn4p1". I hope this helps you find the problem.
> Again, since we don't know what output you really got, it's hard to say
> whether something is wrong or not. You asked for 0 eigenvectory (eigp),
> so you won't get a vecs file in that case.
Thank you very much for your answer. Indeed I used a similar nab script as the one you attached (bench_nm.nab), and as you said my problem was that I was setting eigp the (4th argument in the nmode routine) as 0, and this prevented the vecs file from being created, as I did not ask for any eigenvalue to be computed.
So, in order to get the first 10 normal modes, I changed the following bench_nm.nab script lines:
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
to:
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 10, 0.0, 0.0, 0);
Compiled the nab script, and then executed:
/bench_nm.nab gcn4p1 > stdout_nmodes.txt
Finally I got the vecs file with the normal modes on it, and the stout_nmodes.txt file. The stdout_nmodes.txt contained basically what you posted as output for your "./a.out gcn4p1" execution (I copied most of it below). I believe that the reduced masses for each normal mode should be in this txt file. How can I find these reduced masses? Thank you again,
Lorena
stdout_nmodes.txt
----------------------------------------
Reading parm file (gcn4p1.top)
title:
no velocities were found
mm_options: cut=9999.0
mm_options: rgbmax=9999.0
mm_options: ntpr=1
mm_options: nsnb=9999
mm_options: gb=1
mm_options: diel=C
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.31e-01
ff: 1 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.28e-01
ff: 2 -3591.04 409.68 -346.17 -2195.72 0.00 -1458.84 3.09e-01
ff: 3 -3591.10 409.63 -346.18 -2195.72 0.00 -1458.83 1.34e-01
ff: 4 -3591.11 409.62 -346.18 -2195.72 0.00 -1458.83 1.01e-01
ff: 5 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0039677
For alpha = 0.00000 energy = -3591.1212131189
For alpha = 1.00000 energy = -3591.1325809770
For alpha = 0.99418 energy = -3591.1325813675
For alpha = 0.99423 energy = -3591.1325813675
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0002543
For alpha = 0.00000 energy = -3591.1325813675
For alpha = 1.00000 energy = -3591.1326022869
For alpha = 2.00000 energy = -3591.1325837201
For alpha = 1.02272 energy = -3591.1326022968
For alpha = 1.02202 energy = -3591.1326022970
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000180
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000000
ff: 5 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
Energy = -3.5911326023e+03
RMS gradient = 1.6327027163e-12
dysev time = 60.62 seconds
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 7506.824
Principal moments of inertia in amu-A**2:
289887.38 1439066.88 1492272.08
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
Zero-point vibrational energy: 5735.169
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 2507.471 2161.002 2724.346
translational: 0.888 2.979 52.555
rotational: 0.888 2.979 52.272
vibrational: 6096.827 2155.044 2619.518
ff energy: -3591.133
1 -0.000
2 -0.000
3 -0.000
4 -0.000
5 0.000
6 0.000
7 3.220 0.592 1.986 10.254
8 3.684 0.592 1.986 9.987
9 4.251 0.592 1.986 9.703
10 5.352 0.592 1.986 9.246
11 6.351 0.592 1.986 8.906
12 7.373 0.592 1.986 8.609
13 7.954 0.592 1.986 8.459
14 8.489 0.592 1.986 8.329
.
.
.
3245 3352.525 4.793 0.000 0.000
3246 3354.907 4.796 0.000 0.000
3247 3356.688 4.799 0.000 0.000
3248 3364.660 4.810 0.000 0.000
3249 3688.735 5.274 0.000 0.000
3250 3688.768 5.274 0.000 0.000
3251 3692.834 5.279 0.000 0.000
3252 3692.837 5.279 0.000 0.000
-------------------------------------------------
Date: Mon, 16 Apr 2018 08:59:11 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Simple normal mode analysis in amber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180416125911.ny2b3z65rmzm33dr.vpn-client-172-16-8-12.rutgers.edu>
Content-Type: text/plain; charset="us-ascii"
On Mon, Apr 16, 2018, Lorena.Rosaleny.uv.es wrote:
>
> I'd like to calculate normal modes for a simple protein, and
> I'm trying to use the approach suggested by David Case, with
> the code shown on Amber17 manual page 833 (section 39.4 Second
> derivatives and normal modes). I downloaded the gcn4p1.mc.pdb from the
> $AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/ directory but got
> this when executing:
It's not clear exactly what program you tried to compile and execute.
I've attached my version (bench_nm.nab), along with the output from
"./a.out gcn4p1". I hope this helps you find the problem.
> I also tried to use the script bench_nr.nab with the
> gcn4p1 example. I used the pdb, top and x files from
> $AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/. I added to the
> end of the script the same line that is described in the manual to
> calculate normal modes ( nmodes( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0,
> 0)), but I got a stdout that didn't seem to contain the full information
> on the normal modes (reduced mass, frequency and displacement vectors
> for each atom). I was expecting a vecs file, but didn't get one.
Again, since we don't know what output you really got, it's hard to say
whether something is wrong or not. You asked for 0 eigenvectory (eigp),
so you won't get a vecs file in that case.
..good luck....dac
-------------- next part --------------
Reading parm file (gcn4p1.top)
title:
no velocities were found
mm_options: cut=9999.0
mm_options: rgbmax=9999.0
mm_options: ntpr=1
mm_options: nsnb=9999
mm_options: gb=1
mm_options: diel=C
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.31e-01
ff: 1 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.28e-01
ff: 2 -3591.04 409.68 -346.17 -2195.72 0.00 -1458.84 3.09e-01
ff: 3 -3591.10 409.63 -346.18 -2195.72 0.00 -1458.83 1.34e-01
ff: 4 -3591.11 409.62 -346.18 -2195.72 0.00 -1458.83 1.01e-01
ff: 5 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0039677
For alpha = 0.00000 energy = -3591.1212131189
For alpha = 1.00000 energy = -3591.1325809770
For alpha = 0.99418 energy = -3591.1325813675
For alpha = 0.99423 energy = -3591.1325813675
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0002543
For alpha = 0.00000 energy = -3591.1325813675
For alpha = 1.00000 energy = -3591.1326022869
For alpha = 2.00000 energy = -3591.1325837201
For alpha = 1.02272 energy = -3591.1326022968
For alpha = 1.02202 energy = -3591.1326022970
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000180
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000000
ff: 5 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
Energy = -3.5911326023e+03
RMS gradient = 1.6327027163e-12
dysev time = 10.53 seconds
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 7506.824
Principal moments of inertia in amu-A**2:
289887.38 1439066.88 1492272.08
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
Zero-point vibrational energy: 5735.169
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 2507.471 2161.002 2724.346
translational: 0.888 2.979 52.555
rotational: 0.888 2.979 52.272
vibrational: 6096.827 2155.044 2619.518
ff energy: -3591.133
1 -0.000
2 -0.000
3 -0.000
4 -0.000
5 -0.000
6 0.000
7 3.220 0.592 1.986 10.254
8 3.684 0.592 1.986 9.987
9 4.251 0.592 1.986 9.703
10 5.352 0.592 1.986 9.246
11 6.351 0.592 1.986 8.906
12 7.373 0.592 1.986 8.609
13 7.954 0.592 1.986 8.459
14 8.489 0.592 1.986 8.329
15 9.109 0.592 1.986 8.189
16 9.724 0.592 1.986 8.060
17 10.093 0.592 1.985 7.986
18 11.369 0.592 1.985 7.749
19 11.499 0.592 1.985 7.727
20 12.147 0.592 1.985 7.618
21 12.154 0.592 1.985 7.617
22 12.805 0.592 1.985 7.513
23 13.339 0.592 1.985 7.432
24 13.536 0.592 1.985 7.403
25 13.610 0.592 1.985 7.392
26 14.180 0.592 1.985 7.311
27 14.504 0.592 1.985 7.266
...
3249 3688.735 5.274 0.000 0.000
3250 3688.768 5.274 0.000 0.000
3251 3692.834 5.279 0.000 0.000
3252 3692.837 5.279 0.000 0.000
-------------- next part --------------
// Try some newton-raphson minimization
molecule m;
float x[dynamic], v[dynamic];
float fret;
// Create a molecule from a pdb file and a force-field parameter file.
m = getpdb( argv[2] + ".mc.pdb");
allocate x[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
readparm( m, argv[2] + ".top" );
getxv( argv[2] + ".mc.x", m.natoms, fret, x, v );
// Initialize molecular mechanics..
mm_options("cut=9999.0, rgbmax=9999.0, ntpr=1, nsnb=9999, gb=1, diel=C" );
mme_init(m, NULL, "::ZZZZ", x, NULL);
// conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000 );
// Newton-Raphson minimization
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );
nmode(x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0 );
// mme2_timer();
--
Lorena E. Rosaleny Peralvo, Senior Postdoctoral Researcher
Telf. +0034 963 544 418
Instituto de Ciencia Molecular
Universitat de València
c/ Catedrático José Beltrán Martínez nº 2
46980 Paterna (València)
SPAIN
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Received on Tue Apr 17 2018 - 07:30:02 PDT
