[gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded
Man Hoang Viet
mhviet at ifpan.edu.pl
Tue Dec 15 19:52:15 CET 2015
Hi Alexey,
Thank you for your interesting in my force field conversion. Below content
is how I do implement the force fields step by step, which you may follow
to do double check my work.
I. Get original ff12SB force field from Ambertool15 (free). After untar it
you will have folder amber14, the directory amber14/dat/leap contains all
the force field information.
I.1. look at file amber14/dat/leap/cmd/leaprc.ff12SB you will see some
below lines:
#
# Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod12SB = loadamberparams frcmod.ff12SB
#
# Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
##
It means ff12SB will use parameter from parm10.dat and the modified
parameters from frcmod.ff12SB (you can find these two files in
amber14/dat/leap/parm). The files *.lib are stored in amber14/dat/leap/lib
and they contain information of residues such as number of atoms,
atomtypes, charge ...
I.2. Before doing conversion, we need understand the information in above
files (parm10.dat, ...). The following link will help us on that
http://ambermd.org/formats.html
II. Do convert
Because ff12SB is developed from amber99SB, I use amber99SB as template
and modify to get ff12SB.
The information (atom, bond, angle, improper and dihedrals) for ffbond.itp
and ffnonbond.itp will get from parm10.dat and frcmod.ff12SB. Note that if
the same atom (or bonds, angles ..) shows in both the two files, we will
only keep the ones in frcmod.ff12SB.
The files amin*lib will be used to correct aminoacids.rtp and, while
nucleic12.lib for dna.rtp and rna.rtp.
II.1. Convert atom types (adding new atom type to ffnonbond.itp)
The first part in parm10.dat and frcmod.ff12SB introduced atomtypes and
their mass, while the last part give us parameters for 6-12 interaction.
The last part of parm10.dat:
...
N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ CP CS
MOD4 RE
H 0.6000 0.0157 !Ferguson base pair geom.
...
N 1.8240 0.1700 OPLS
...
END
The line "N NA N2 N* NC NB NT NY" indicates all those atoms share
the same parameters. It is similar for the line "C* CA CB CC CD CK
CM CN CQ CR CV CW CY CZ CP CS"
The line "N 1.8240 0.1700" means van der Waals radius and
epsilon of atom N are 1.8240 Å and 0.1700 kcal/mol, respectively ---> in
gromacs (ffnonbond.itp) atom N will has
sigma=1.7818*1.8240*10^1=3.25000e-1, and epsilon=0.1700*4.184=7.11280e-1
(kJ/mol). The constant 1.7818=2/{2^(1/6)}.
By this way, it is easy to add some new atomtypes such as CX, 2C, 3C ..
II.2. Convert bonds and angles (ffbond.itp)
This is a simple work, because we only need consider unit from kcal in
amber to kJ in gromacs for the "harmonic force constants".
II.3. Convert impropers
in AMBER:
;i j k l PK Phase PN
CA-CA-CA-OH 1.1 180. 2.
in gromacs: a improper is dihedraltype 4
;i j k l func phase kd pn
CA CA CA OH 4 180.00 4.60240 2
for improper, gromacs define as dihedral by function type 4 and
kd=PK*4.184
II.4. Convert dihedrals:
Some examples for dihedrals in amber:
;i j k l IDIVF PK PHASE PN
X -CI-OS-X 3 1.150 0.0 3.
X -CX-N3-X 9 1.40 0.0 3.
X -C4-N*-X 4 7.40 180.0 2.
CX-2C-S -S 2 0.386 137.8 -4. Cyx chi2
CX-2C-S -S 2 0.337 12.0 -3.
CX-2C-S -S 2 1.166 -40.1 -2.
CX-2C-S -S 2 1.389 -112.7 1.
2C-S -S -2C 1 0.193 32.5 -4. Cyx disulf
2C-S -S -2C 1 0.957 -0.5 -3.
2C-S -S -2C 1 4.542 1.5 -2.
2C-S -S -2C 1 0.543 -25.0 1.
convert in to gromacs
;i j k l func phase kd pn
X CI OS X 9 0.0 1.60387 3
X CX N3 X 9 0.0 0.65084 3
X C4 N* X 9 180.0 7.74040 2
CX 2C 2C S 9 86.9 0.63178 4
CX 2C 2C S 9 79.7 0.63178 3
CX 2C 2C S 9 8.3 0.99579 2
CX 2C 2C S 9 -3.8 1.63594 1
2C S S 2C 9 32.5 0.80751 4
2C S S 2C 9 -0.5 4.00409 3
2C S S 2C 9 1.5 19.00373 2
2C S S 2C 9 -25.0 2.27191 1
In gromacs dihedrals func=9, kd=PK*4.184/IDIVF.
II.5. Correct amino acids, dna and rna by new atoms type.
In this part, I have compared residues in gromacs to residues in amber and
changed some atomtypes to make sure thay are the same in amber and
gromacs.
The work for the ff14SB conversion is similar.
I have written some codes (scripts and Fortran) to automatically convert
bonds, angles, dihedrals and compare residues. But adding new atomtypes
and correcting them in residues I have to do by hand.
PS, I am sorry, I forgot changing the forcefield.doc file, but it is not
important :).
> From: Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] amber force field ff12SB and ff14SB for
> gromacs uploaded
> Message-ID: <99d36c6236750208c9b9ccd305836cad at omrb.pnpi.spb.ru>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi!
>
> Thank you forforcefield conversion! But how you checked that all
energies are same?
>
> PS problems with different ions can be simply fixed with set of defines
>PPS also seems like forcefield.doc in ff directory are wrong. It states
>that it is still amber99sb forcefield
>
> Man Hoang Viet ????? 14-12-2015 06:56:
>> Dear gromacs users,
>> The amber force fields, ff12SB abd ff14SB, for gromacs were uploaded.
>>From
>> my side, I may confirm the accuracy of my converting for every atoms,
bonds, angels, impropers and diherals parameters, but it will be much
>> >> better if some ones can double check it (I will provide my codes,
>>strategy
>> and explanation of the converting for gromacs users who really want to
>>do
>> the checking work). Please note that the parameters of ions (such as
>>Na+,
>> Mg+ ...) will be differences in the different water models. Here, the
>>ion
>> parameters are for TIP3P water model. Therefore you will need edit ion
parameters if you wan to use ions in other water models.
>> Yours sincerely,
>> Viet Man
>> Postdoctoral Research Associate,
>> Physics Department, NCSU
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
> mailto:alexxyum at gmail.com
> mailto:alexxy at omrb.pnpi.spb.ru
--
Man Hoang Viet
Postdoctoral research associate.
Physics Department, NCSU
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