[AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed?

From: Chris King <chrisk1.uw.edu>
Date: Thu, 24 Feb 2011 15:15:31 -0800

Hello there! I've been running 3D-RISM calculations to benchmark our
empirical model in Rosetta, and was wondering about the energy output when
mme() is called. Specifically, I see a value in the column for "genBorn"
(see below), even though I have not turned on generalized born
electrostatics in my *.nab file ( the default value for "gb" is supposedly

Is this value being calculated anyways, or is a different value been
displayed in this column...
Is the 3D-RISM solvation free energy being computed by amber?

Thank you so much for any help!
Chris King
Baker Lab
University of Washington - Seattle

Sample output:

      iter Total bad vdW elect nonpolar genBorn
ff: 0 128839.80 133035.26 2485.56 -8753.09 0.00 2072.07

NAB script:

// carry out 1 step molecular dynamics
molecule m;
float m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];
float dgrad, energy, dummy[2];
string F, F2;

F = "HA35.pdb";
m = getpdb_prm( F, "leaprc.ff99SB", "", 0 );
allocate m_xyz[ 3*m.natoms ]; allocate f_xyz[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
setxyz_from_mol( m, NULL, m_xyz );
mm_options("ntpr=1, cut=999.0"); //No solute-solute CUTOFF

//rism stuff
mm_options("rism=1, closure=1, buffer=10"); //Use 3D-RISM-KH
mm_options("grdspcx=1.0, grdspcy=1.0, grdspcz=1.0"); //Use 3D-RISM-KH
mm_options("mdiis_del=0.7, mdiis_vec=5, mdiis_method=1, maxstep=1000,
mm_options("xvvfile=../wat.xvv"); //1D-RISM input
mm_options("tolerance=1e-5"); //Low tolerance
mm_options("solvcut=999.0"); //No solute-solvent
mm_options("centering=2"); //Center solute
mm_options("ntwrism=1, guvfile=guv, huvfile=huv, cuvfile=cuv");

// MD simulation
mme_init( m, NULL, "::ZZZ", dummy, NULL );
mm_options("zerov=1, tempi=0.0");
md( 3*m.natoms, 1, m_xyz, f_xyz, v, mme );
energy = mme( m_xyz, f_xyz, 1 );
setxyz_from_mol( m, NULL, m_xyz );
putpdb( "HA35.amber.pdb", m );
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Received on Thu Feb 24 2011 - 15:30:04 PST
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