Dear All,
I was playing with different water models such as the TIP4PEW water parameters.
Yet, it seems that leap does not create the correct parameters for this water
model. I see that the LJ and bond parameters are correctly added in the prmtop
file. Yet, I do not see any angular parameters for TIP4PEW in the prmtop file.
The frcmod file of TIP4PEW uses the following parameters:
------------- frcmod.tip4pew -------------
This is the additional/replacement parameter set for TIP4P
MASS
OW 16.0
EP 0.0
BOND
OW-EP 553.000 0.1250
OW-HW 553.0 0.9572
HW-HW 553.0 1.5136
ANGLE
HW-OW-EP 0.0 120.0
HW-OW-HW 100. 104.52
HW-HW-OW 0. 127.74
DIHE
X -HW-OW-X 2 0.0 0.0 1.0
NONBON
OW 1.775931 0.16275
EP 1.0 0.0
--------------------------------------------------------
The leap script I use for the TIP4PEW water model is as follows:
--------------- tleap.in -------------------
source oldff/leaprc.rna.ff99
loadamberparams
/home/iyildirim/programs/amber16/dat/leap/parm/frcmod.ionsjc_tip4pew
loadamberparams /home/iyildirim/programs/amber16/dat/leap/parm/frcmod.tip4pew
loadoff /home/iyildirim/programs/amber16/dat/leap/lib/atomic_ions.lib
loadoff /home/iyildirim/programs/amber16/dat/leap/lib/tip4pewbox.off
set default PBradii mbondi2
mol = loadpdb model_1.pdb
addions mol Na+ 0
solvateOct mol TIP4PEWBOX 11.00
addions mol Na+ 5
addions mol Cl- 5
savepdb mol model_xleap.pdb
saveAmberParm mol prmtop inpcrd
quit
--------------------------------------------
This should add the TIP4PEW water model parameters to the prmtop, am I correct?
If yes, I do not understand why the angular parameters are missing in the
prmtop file. Just creating a prmtop file for TIP4PEWBOX has the following
entries:
.
.
.
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.53000000E+02 5.53000000E+02 5.53000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
9.57200000E-01 1.25000000E-01 1.51360000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
.
.
.
Any suggestions? Thanks in advance.
Cheers,
Ilyas Yildirim, Ph.D.
---------------------------------------------------------
= Assistant Professor =
= Department of Chemistry & Biochemistry =
= Florida Atlantic University =
= 5353 Parkside Drive, Building MC17, Jupiter, FL 33458 =
= =
= Phone: +1(561)799-8325 | E-mail: iyildirim.fau.edu =
---------------------------------------------------------
= Group Website: http://cosweb1.fau.edu/~iyildirim =
= =
=
http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
---------------------------------------------------------
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Received on Wed Jul 12 2017 - 09:00:02 PDT
