On Tue, Sep 21, 2010 at 14:36, case <case.biomaps.rutgers.edu> wrote:
> The best thing is to edit the pdb file, and change the atom and residue names
> to match those in the Amber library.
I have done that, and everything seemed to be fine, until I actually
looked at the topology while using a flexible water parametrization.
The frcmod information doesn't seem to be being applied at all.
PDB:
[...]
ATOM 1 O WAT 1 75.670 75.870 35.030 1.00 0.00
ATOM 2 H1 WAT 1 75.750 75.690 36.010 1.00 0.00
ATOM 3 H2 WAT 1 74.720 75.780 34.750 1.00 0.00
ATOM 4 O WAT 2 79.110 75.960 33.670 1.00 0.00
ATOM 5 H1 WAT 2 78.690 76.830 33.930 1.00 0.00
ATOM 6 H2 WAT 2 78.430 75.390 33.210 1.00 0.00
[...]
TLEAP:
source leaprc.ff03.r1
loadamberparams frcmod.spcfw
WAT = SPF
CLUSTER = loadpdb conf.pdb
saveamberparm CLUSTER conf.top conf.crd
quit
FRCMOD.SPCFW:
Parameter set for SPC/Fw of Wu, Tepper & Voth, J. Chem. Phys. 124:024503, 2006.
MASS
OW 16.0
BOND
OW-HW 529.58 1.0120 SPC/E water
HW-HW 0.0 1.6330 SPC/E water
ANGLE
HW-OW-HW 37.95 113.24
DIHE
NONBON
OW 1.7767 0.1554
TOPOLOGY OUTPUT:
[...]
%FORMAT(5E16.8)
1.63300000E+00 1.01200000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
[...]
What am I doing wrong?
Anthony
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Received on Wed Sep 22 2010 - 12:00:05 PDT
