[gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded
Justin Lemkul
jalemkul at vt.edu
Tue Dec 15 19:55:20 CET 2015
On 12/15/15 1:52 PM, Man Hoang Viet wrote:
> 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 :).
>
The concern is less about the method of conversion; these types of programs are
reasonably straightforward to write. The concern is always that the energies
and forces calculated in one program match the other. The simplest thing to do
is run some single-point energy evaluations in AMBER and GROMACS. If they
match, your conversion is successful. If they don't, you have a problem with
the integrity of the GROMACS files. You say above that you "make sure that they
are the same in AMBER and GROMACS" but you don't specify what that means.
Visual inspection of the contents? Or actual quantitative assessment?
-Justin
>
>> 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
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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