Dear all,
this is NAB code which could be used for the same purpose like mm_PBSA
routine. Of course just
considering GB calculation (PB is not implemented in NAB if I am not
wrong). In other
words this code can calculate the total energy of the system in implicit
solvent and
also entropy so it could be used similarly like mm_PBSA for calculation of
dG. I have
just one question regarding to the output of this code please see below.
--------------------------------------------------------------------------------------
molecule m;
float x[8580],y[6258],z[2322], fret;
int N_max;
N_max=10000;
m = getpdb( "com_50_min.pdb");
readparm( m, "com.prmtop");
getxyz( "snap_com.crd_min.50", 2860 , x );
mm_options( "cut=999., ntpr=100, nsnb=99999, diel=C, gb=1, dielc=1.0" );
mme_init( m, NULL, "::Z", x, NULL);
setxyz_from_mol( m, NULL, x );
// conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.001, 0.01, N_max );
// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
newton( x, 3*m.natoms, fret, mme , mme2, 0.00000001, 0.0, 2 );
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
----------------------------------------------------------------------------------------
PART OF THE OUTPUT OF THE ABOVE CODE
---------------------------------------------------------------------------
Temperature: 298.150
Pressure: 1.000
Mass: 21322.046
Principal moments of inertia in amu-A**2:
2888204.05 5375242.35 6139589.11
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
Zero-point vibrational energy: 14969.383
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 15530.815 5850.913 6845.291
translational: 0.888 2.979 55.665
rotational: 0.888 2.979 57.268
vibrational: 15927.237 5844.956 6732.359
----------------------------------------------------------------------------
There is clearly written "Temperature", "Pressure" which can be set
probably in function
mm_options() - for example temperature using parameter TEMPI parameter. If
nothing is set, then the
above defaults are used.
In mm_PBSA routine there is no chance (if I am not wrong) to set this
thermodynamics parameters so
there are probably used some defaults. But what if my simulations was done
under slightly different
conditions - for example T=310K instead defaul T=298K ?
Just regarding TS calculation which is the output of NN mm_PBSA analysis.
It is OK in this case just
this transformation TS(310K)=310*TS(298K)/298 ...?
Thanks in advance for any relevant comments.
With the best regards
Marek
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Mon Jul 06 2009 - 08:33:18 PDT
