Thanks Dan, this worked.
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 =
---------------------------------------------------------
On Wed, 12 Jul 2017, Daniel Roe wrote:
> 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
>>>
>>
>> _______________________________________________
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>> AMBER-Developers.ambermd.org
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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
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Wed Jul 12 2017 - 09:30:04 PDT
