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Re: [lammps-users] Amber FF
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Re: [lammps-users] Amber FF


From: "James Kress" <jimkress_58@...5633...>
Date: Tue, 3 Oct 2017 22:19:57 -0400

Try these:

               

                s:\home\amber16\dat\chamber\par_all22_prot.inp   4/7/2017   3:08:21 PM   163641

    336     !V(Urey-Bradley) = Kub(S - S0)**2

    340     !Kub: kcal/mole/A**2 (Urey-Bradley)

               

                s:\home\amber16\dat\chamber\par_all36_carb.prm   4/7/2017   3:08:21 PM   146931

    358     !V(Urey-Bradley) = Kub(S - S0)**2

    361     !Kub: kcal/mole/A**2 (Urey-Bradley)

               

                s:\home\amber16\dat\chamber\toppar_water_ions.str   4/7/2017   3:08:21 PM   9141

    195     !V(Urey-Bradley) = Kub(S - S0)**2

    199     !Kub: kcal/mole/A**2 (Urey-Bradley)

               

                s:\home\amber16\dat\chamber\par_all27_prot_na.prm   4/7/2017   3:08:21 PM   242278

    512     !V(Urey-Bradley) = Kub(S - S0)**2

    516     !Kub: kcal/mole/A**2 (Urey-Bradley)

               

                s:\home\amber16\dat\chamber\par_all36_prot.prm   4/7/2017   3:08:21 PM   184930

    345     !V(Urey-Bradley) = Kub(S - S0)**2

    349     !Kub: kcal/mole/A**2 (Urey-Bradley)

 

 

Jim

 

 

From: jewett.aij@...24... [mailto:jewett.aij@...24...] On Behalf Of Andrew Jewett
Sent: Tuesday, October 03, 2017 9:58 PM
To: Jim Kress <jimkress_58@...5633...>
Cc: Hossein Geraili <geraili.hsn@...24...>; LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>
Subject: Re: [lammps-users] Amber FF

 

Good to know the existence of the GAFF2 force field.  I was unaware.  Added it to moltemplate today.  Thanks!

 

(...but I still didn't see any of Urey-Bradley terms that Hossein mentioned.)

-andrew

 

On Tue, Oct 3, 2017 at 6:13 PM, James Kress <jimkress_58@...5633...> wrote:

You’ll find gaff and gaff2 in amber16/dat/leap/parm

 

Jim

 

 

From: Andrew Jewett [mailto:jewett@...1937...]
Sent: Tuesday, October 03, 2017 8:05 PM
To: Hossein Geraili <geraili.hsn@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>
Subject: Re: [lammps-users] Amber FF

 

 

 

On Tue, Oct 3, 2017 at 7:19 AM, Hossein Geraili <geraili.hsn@...24...> wrote:

E = K (theta - theta0)^2 + K_UB (r_13 - r_UB)^2
K_UB and r_UB(cross-term accounting for angle bending using 1,3 nonbonded interactions). How can I calculate these?

 

On Tue, Oct 3, 2017 at 5:33 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

 

On Tue, Oct 3, 2017 at 9:37 AM, Hossein Geraili <geraili.hsn@...24...> wrote:

Dear Lammps users,

I am using Amber force field optimized for my molecule, and it(in the article) has only two parameters for the angle. In the lammps section Howto for Amber angle_style charmm in introduced, but for charmm angle_style one should specify 4 parameters( 2Urey_Bradley parameters). I simulated with harmonic and I get a big error. Any idea where should I find these Urey_Bradley parameters? Actually the "distance between the 1,3 atoms in the harmonic potential" which is the Rub(one of the parameters, I can find. But, what about the force constant?

 

here is the $5000 question: what is the force constant of term that does not exist?

 

axel.

 

 

    For what it's worth, there are no Urey-Bradley parameters listed in the "gaff.dat" file distributed with AmberTools.  (I have not looked at the other AMBER force-field files.)  Don't know if this helps.  Where are you reading about these Urey-Bradley parameters?

 

-andrew