Hi,
I am trying to perform TI on a molecule comprised of same type of atoms. I
have set every atom type to H1 and I call an external .frcmod file where I
specify the parameters mass, bond constants, angle dihedral etc. I bond the
nearest neighbor (1-2) type bonds. My molecule is such that each atom is
connected to exactly two other atoms in the molecule. Then I solvate the
molecule in a TIP3P box. I set ntf=ntc=2 and perform the TI. As I specify
the atom type to H1 I was expecting that the bond length doesn't change in
these rings, but that's not the case. Is there a way to use shake to
perform TI to compute the hydration free energy?
Thanks,
Abhishek
----------------------------------------
Here is my frcmod file:
----------------------------------------
MASS
H1 12.01
BOND
H1-H1 478.4 1.4
ANGLE
H1-H1-H1 67.200 60.00
DIHE
X -H1-H1-X 1 14.500 0.000 1.000
NONBON
H1 1.3870 0.0157
--------------------------------------------------------------------------------------------------
Here is the leap file use to generate the topology and coordinate file:
--------------------------------------------------------------------------------------------------
source /home/shared_utilities/amber11/dat/leap/cmd/leaprc.ff99SB
loadamberparams blabla.frcmod
mol = loadpdb whatever.pdb
set mol.1.CC1 type H1
set mol.1.CC2 type H1
set mol.1.CC3 type H1
set mol.1.CC1 charge 0.800
set mol.1.CC2 charge -0.400
set mol.1.CC3 charge -0.400
bond mol.1.CC1 mol.1.CC2
bond mol.1.CC2 mol.1.CC3
bond mol.1.CC3 mol.1.CC1
solvatebox mol TIP3PBOX 12.0
saveamberparm mol mol_wat0.prmtop mol_wat0.inpcrd
saveamberparm mol mol_wat1.prmtop mol_wat1.inpcrd
savepdb mol tip3pbox.pdb
quit
--------------------------------------------------------
Here is a sample production input file:
--------------------------------------------------------
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 1000, ntwr = 10000, ntwx = 1000, ntave=1000,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
nstlim =1000000, dt = 0.002,
ig = 23563,
temp0 = 300.0, tempi = 300.0,
ntt = 3, gamma_ln = 2,
icfe=1, clambda = 0.04691,
ifsc=0,
crgmask=''
/
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Received on Wed Oct 03 2012 - 15:00:02 PDT
