Amber FF

Hossein_Geraili · October 3, 2017, 1:37pm

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?
Best

akohlmey · October 3, 2017, 2:03pm

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.

Hossein_Geraili · October 3, 2017, 2:19pm

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?

Best

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Andrew_Jewett1 · October 4, 2017, 12:04am

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?

<#m_-5048133961489861109_>

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

_James_Kress · October 4, 2017, 1:13am

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

Jim

Andrew_Jewett1 · October 4, 2017, 1:57am

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

_James_Kress · October 4, 2017, 2:19am

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

Andrew_Jewett1 · October 4, 2017, 3:22am

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.)

Andrew_Jewett1 · October 4, 2017, 10:01pm

Dear Hossein

The moltemplate implementation of the GAFF forcefield has been tested by several people and they say it is accurate now. (It wasn’t at first. The GAFF2 force field probably works as well because it was automatically converted from a file with an identical file format as GAFF. But it has not yet been tested.)

The main issues with using GAFF/GAFF2 in moltemplate are:

If my understanding is correct, it was not intended for proteins and nucleic acids. It was intended for small organic molecules. Hopefully that’s not a problem for you.
Moltemplate does not calculate the partial charge on each atom correctly for the AMBER force fields. Moltemplate is a (relatively) simple database lookup program. It does not perform quantum-chemistry calculations to determine atomic charges (AmberTools does this). You will have to use AmberTools or some other quantum code to calculate them (or lookup the partial charges from “oplsaa.lt”. That’s what the AMBER examples which come with moltemplate do.) . Afterwards, you can use commands like
set atom 70 charge -0.212

to assign partial charges to each atom.

For details, see http://lammps.sandia.gov/doc/set.html)

and

http://ambermd.org/antechamber/gaff.html

Cheers
-andrew