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
>
> _______________________________________________
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>
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Received on Wed Jul 12 2017 - 09:30:03 PDT
