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


From: Andrew Jewett <jewett@...1937...>
Date: Tue, 3 Oct 2017 20:22:19 -0700

Hossein, if you are wondering where these files are, you can download them from:
http://ambermd.org/AmberTools16-get.html
Unpack the file, and navigating to the "amber16/dat/chamber" subdirectory.
I have no idea if this helps or is even relevant.  So far, I've only played with GAFF.

andrew
(Perhaps I'll attempt to convert these other forcefields later.)

On Tue, Oct 3, 2017 at 7:19 PM, James Kress <jimkress_58@...5633...> wrote:

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@...5634......>
Cc: Hossein Geraili <geraili.hsn@...24...>; LAMMPS Users Mailing List <lammps-users@...42...e.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@...42...e.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