I would like to clarify that the parameters for TIP3P water are not leaded.
In the log file I get this:
>> # to use ions for TIP5P, you will need to use a different frcmod below
>> # If desired, see the AMBER manual for additional ion force field
options.
>> ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
>
> source leaprc.water.opc
----- Source: /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.opc
----- Source of /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.
opc done
Why are those read?
Lastly, is the 12-6 LJ potential used for the OPC water model (and any 3
point charge rigid model)?
Thank you
L.
Also, is the UNKNOWN ATOM TYPE:EP a problem? The topology file gets created.
---------- Původní e-mail ----------
Od: Loki <Vellryba.seznam.cz>
Komu: AMBER Mailing List <amber.ambermd.org>
Datum: 3. 7. 2020 19:04:54
Předmět: Re: [AMBER] LJ potential for OPC water model
"
Dear Matias,
so Mi/Mertz for the water. Thank you, yes that does make sense.
L.
---------- Původní e-mail ----------
Od: Matias Machado <mmachado.pasteur.edu.uy>
Komu: AMBER Mailing List <amber.ambermd.org>
Datum: 3. 7. 2020 17:39:11
Předmět: Re: [AMBER] LJ potential for OPC water model
"Dear Loki,
It's right here in your log:
>> loadAmberParams frcmod.ionsjc_tip4pew
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham
JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip4pew
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
ions234lm_126_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water
model (12-6 normal usage set)
>>
You are using both set of parameters... for monovalent ions: Joung &
Cheatham, for divalent-tetravalent: Li/Mertz
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Loki" <Vellryba.seznam.cz>
Para: amber.ambermd.org
Enviados: Viernes, 3 de Julio 2020 9:07:04
Asunto: [AMBER] LJ potential for OPC water model
Dear all,
I am a bit confused regarding the use of the LJ potential with OPC water
model.
My leap infile:
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.GLYCAM_06j-1
source leaprc.water.opc
foo=loadpdb "min_1.pdb"
check foo
WAT=OPC
......
Can I ask which parameters am I actually using? In the manual I read there
are several available, some by Li, Merz and some by Young and Cheatham. I
cant work it out from the log file:
> source leaprc.water.opc
----- Source: /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.opc
----- Source of /s/amber/amber18/CentOS7/amber18/dat/leap/cmd/leaprc.water.
opc done
>> #
>> # Load water and ions for OPC + Joung-Chetham monovalent ions for
>> # tip4pew + Li/Merz highly charged ions (+2 to +4, 12-6 normal
usage set)
>> # for tip4pew
>> #
>> addAtomTypes {
>> { "F-" "F" "sp3" }
>> { "Cl-" "Cl" "sp3" }
>> { "Br-" "Br" "sp3" }
>> { "I-" "I" "sp3" }
>> { "Li+" "Li" "sp3" }
>> { "Na+" "Na" "sp3" }
>> { "K+" "K" "sp3" }
>> { "Rb+" "Rb" "sp3" }
>> { "Cs+" "Cs" "sp3" }
>> { "Mg+" "Mg" "sp3" }
>> { "Tl+" "Tl" "sp3" }
>> { "Cu+" "Cu" "sp3" }
>> { "Ag+" "Ag" "sp3" }
>> { "Be2+" "Be" "sp3" }
>> { "Cu2+" "Cu" "sp3" }
>> { "Ni2+" "Ni" "sp3" }
>> { "Pt2+" "Pt" "sp3" }
>> { "Zn2+" "Zn" "sp3" }
>> { "Co2+" "Co" "sp3" }
>> { "Pd2+" "Pd" "sp3" }
>> { "Ag2+" "Ag" "sp3" }
>> { "Cr2+" "Cr" "sp3" }
>> { "Fe2+" "Fe" "sp3" }
>> { "Mg2+" "Mg" "sp3" }
>> { "V2+" "V" "sp3" }
>> { "Mn2+" "Mn" "sp3" }
>> { "Hg2+" "Hg" "sp3" }
>> { "Cd2+" "Cd" "sp3" }
>> { "Yb2+" "Yb" "sp3" }
>> { "Ca2+" "Ca" "sp3" }
>> { "Sn2+" "Sn" "sp3" }
>> { "Pb2+" "Pb" "sp3" }
>> { "Eu2+" "Eu" "sp3" }
>> { "Sr2+" "Sr" "sp3" }
>> { "Sm2+" "Sm" "sp3" }
>> { "Ba2+" "Ba" "sp3" }
>> { "Ra2+" "Ra" "sp3" }
>> { "Al3+" "Al" "sp3" }
>> { "Fe3+" "Fe" "sp3" }
>> { "Cr3+" "Cr" "sp3" }
>> { "In3+" "In" "sp3" }
>> { "Tl3+" "Tl" "sp3" }
>> { "Y3+" "Y" "sp3" }
>> { "La3+" "La" "sp3" }
>> { "Ce3+" "Ce" "sp3" }
>> { "Pr3+" "Pr" "sp3" }
>> { "Nd3+" "Nd" "sp3" }
>> { "Sm3+" "Sm" "sp3" }
>> { "Eu3+" "Eu" "sp3" }
>> { "Gd3+" "Gd" "sp3" }
>> { "Tb3+" "Tb" "sp3" }
>> { "Dy3+" "Dy" "sp3" }
>> { "Er3+" "Er" "sp3" }
>> { "Tm3+" "Tm" "sp3" }
>> { "Lu3+" "Lu" "sp3" }
>> { "Hf4+" "Hf" "sp3" }
>> { "Zr4+" "Zr" "sp3" }
>> { "Ce4+" "Ce" "sp3" }
>> { "U4+" "U" "sp3" }
>> { "Pu4+" "Pu" "sp3" }
>> { "Th4+" "Th" "sp3" }
>> }
>> loadOff atomic_ions.lib
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/atomic_ions.
lib
Loading: AG
Loading: AL
Loading: Ag
Loading: BA
Loading: BR
Loading: Be
Loading: CA
Loading: CD
Loading: CE
Loading: CL
Loading: CO
Loading: CR
Loading: CS
Loading: CU
Loading: CU1
Loading: Ce
Loading: Cl-
Loading: Cr
Loading: Dy
Loading: EU
Loading: EU3
Loading: Er
Loading: F
Loading: FE
Loading: FE2
Loading: GD3
Loading: H3O+
Loading: HE+
Loading: HG
Loading: HZ+
Loading: Hf
Loading: IN
Loading: IOD
Loading: K
Loading: K+
Loading: LA
Loading: LI
Loading: LU
Loading: MG
Loading: MN
Loading: NA
Loading: NH4
Loading: NI
Loading: Na+
Loading: Nd
Loading: PB
Loading: PD
Loading: PR
Loading: PT
Loading: Pu
Loading: RB
Loading: Ra
Loading: SM
Loading: SR
Loading: Sm
Loading: Sn
Loading: TB
Loading: TL
Loading: Th
Loading: Tl
Loading: Tm
Loading: U4+
Loading: V2+
Loading: Y
Loading: YB2
Loading: ZN
Loading: Zr
>> loadOff solvents.lib
Loading library: /s/amber/amber18/CentOS7/amber18/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: OP3
Loading: OPC
Loading: OPC3BOX
Loading: OPCBOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = OPC
>> WAT = OPC
>> loadAmberParams frcmod.opc
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871)
(UNKNOWN ATOM TYPE: EP)
>> loadAmberParams frcmod.ionsjc_tip4pew
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham
JPCB (2008)
>> loadAmberParams frcmod.ions234lm_126_tip4pew
Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
ions234lm_126_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water
model (12-6 normal usage set)
>>
I also saw TIP3P parameters being loaded and I am not sure which ones are
actually used.
Thank you
L.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
"
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
"
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 03 2020 - 11:30:05 PDT
