Sorry, didn't read your original post closely enough. Tleap is
assuming you want a rigid water model (this is the default behavior),
therefore there are no angle terms needed. You need to enter:
set default FlexibleWater on
to change this behavior I think.
-Dan
On Wed, Jul 12, 2017 at 12:08 PM, Ilyas Yildirim <iyildirim.fau.edu> wrote:
> I still cannot see angular parameters defined for the water molecules even
> when I do i) set WAT=TP4 or ii) source leaprc.water.tip4pew. As I wrote
> before, interestingly, however, the bond and LJ parameters are correctly
> described in the prmtop file. I have amber16 installed (and I think
> AmberTools 16). Not sure if this is an issue with the version of
> AmberTools I am using!?
>
> 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 =
> ---------------------------------------------------------
>
> On Wed, 12 Jul 2017, Daniel Roe wrote:
>
>> 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 =
>>> ---------------------------------------------------------
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>>
>> --
>> -------------------------
>> 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
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
-------------------------
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 - 09:30:03 PDT
