Hi,
I think you are missing this in your script:
WAT=TP4
-Dan
PS - With the latest versions of AT you can load TIP4P params via
'source leaprc.water.tip4pew'.
On Wed, Jul 12, 2017 at 11:41 AM, Ilyas Yildirim <iyildirim.fau.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jul 12 2017 - 09:00:03 PDT
