AMBER Archive (2009)

Subject: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ?

From: Marek Maly (
Date: Wed Jun 10 2009 - 05:33:59 CDT

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;


   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);



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


Tato zpráva byla vytvořena převratným poštovním klientem Opery:

AMBER mailing list