Hi Anna,
AMBER angle and dihedral force constants are usually specified in
kcal/mol-rad^2, while the equilibrium values are in degrees. Try
multiplying/dividing by (pi/180)^2.
Regards,
Brian
On Tue, Mar 26, 2013 at 5:41 AM, Anna Marabotti <amarabotti.unisa.it> wrote:
> Dear Amber users,
> many thanks for your answer, I think that Jason's suggestion is correct.
>
> Now I have another question for you. I compared the forces calculated
> with Antechamber using Amber99SB classical forcefield (not GAFF, since
> my molecule must be integrated into the protein's parameters) with those
> present in Gromacs-implemented Amber99SB forcefield. In that forcefield,
> I found that, apart from the difference of 4.184x2 of which I talked
> previously, the values of force constants for angles are all "exact"
> numbers, link 40, 50, 70, 120 etc. Instead, the force constant I have
> for my molecules are all numbers such as 42.458, 55.664, 74.987, 122.754
> and so on. In a first time, I thought that the problem was in Gromacs
> implementation of Amber forcefield. But when I had a look at the
> parm99.dat file from Amber ff, I found that force constant for angles
> are exactly 80, 70, 40, 120..., so I have to think that Antechamber's
> parameterization is not in line with Amber99SB parameters.
> The Gromacs users suggested me to check for the correctness of
> Antechamber parameterization with you, so I'm coming here with my question.
>
> My .pdb molecule is formed by my chromophore (CFY) and the two residues
> flanking it in the protein sequence, in order to avoid problems with
> terminals of my molecule. My starting molecule is then Val63-CFY-His68.
> To parameterize my molecule, I did the following steps (extracted from
> Antechamber SUSTIVA tutorial):
>
> antechamber -i V63-CFY-H68.pdb -fi pdb -o V63-CFY-H68.mol2 -fo mol2 -c
> bcc -s 2 (to obtain charges)
>
> *parmchk -i V63-CFY-H68.mol2 -f mol2 -o V63-CFY-H68.frcmod* (no missing
> parameters referred to CFY)
>
> *$tleap -f leaprc.ff99SB
> *I did not use "*source leaprc.gaff*" since I want to use the
> "classical" Amber99SB force field.
>
> >CFY = loadmol2 V63-CFY-H68.mol2
>
> *>loadamberparams **V63-CFY-H68.frcmod*
>
> *>**saveoff CFY ***V63-CFY-H68*.lib *
>
> >saveamberparm CFY *V63-CFY-H68*.prmtop *V63-CFY-H68*.inpcrd
>
> Did I use the correct procedure to obtain parameters for my molecule
> compatible with the Amber99SB forcefield? Or should I use different
> commands in order to implement this "classical" force field? Do I have
> to "constrain" somehow Antechamber and tLeap in order to work with
> Amber99SB forcefield?
>
> Many thanks again and best regards
> Anna
>
> ______________________________________________
> Anna Marabotti, Ph.D.
> Assistant Professor
> Department of Chemistry and Biology
> University of Salerno
> Via Ponte don Melillo
> 84084 Fisciano (SA)
> Italy
> Phone: +39 089 969583
> Fax: +39 089 969603
> E-mail: amarabotti.unisa.it
> Skype: annam1972
>
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>
> Il 25/03/2013 20:00, amber-request.ambermd.org ha scritto:
> > Message: 23
> > Date: Mon, 25 Mar 2013 08:27:59 -0400
> > From: Jason Swails<jason.swails.gmail.com>
> > Subject: Re: [AMBER] problems in parameters calculated with AMBER
> > To: AMBER Mailing List<amber.ambermd.org>
> > Message-ID:
> > <CAEk9e3rPiKhHU74Q-Vdj6a=
> RMn9j8FdJqRFFZG_bfAMif8GGoA.mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Mon, Mar 25, 2013 at 8:12 AM, Anna MARABOTTI<amarabotti.unisa.it>
> wrote:
> >
> >> >
> >> >
> >> >Dear Amber users,
> >> >
> >> >I am new to this list, and I am not currently
> >> >using Amber. I'd need an help to understand a problem that I have with
> >> >Antechamber suite.
> >> >
> >> >I want to calculate parameters for a cofactor of a
> >> >green fluorescent proteins, using Amber99SB ff, in order to implement
> >> >these parameters into the ff used by GROMACS. I used Antechamber to
> >> >perform calculations, following the Antechamber tutorial. I obtained
> the
> >> >.mol2, .frcmod, .prmtop and .inpcrd files regularly.
> >> >
> >> >To implement
> >> >these parameters into the Amber99sb forcefield, I have to convert them
> >> >since the units are not equal: in the .frcmod I understand that, e.g.
> >> >the bond force constant is expressed in kcal/(mol A^2), whereas in the
> >> >parameters set in the AMBER99SB forcefield for GROMACS, the force
> >> >constant is expressed in KJ/(mol nm^2). Therefore, roughly to convert
> my
> >> >Amber parameters into Gromacs parameters, I should multiply them by
> >> >approx. 418.4.
> >> >
> >> >I checked the parameters present in both files, and I
> >> >see that the difference is not approx. 400, but approx. 800. I don't
> >> >understand what is the source of this factor of 2. I obviously asked
> the
> >> >same to GROMACS users, but I'm checking also with you. Are parameters
> in
> >> >.frcmod file referred only to one atom, or to both (so I have to
> >> >multiply - or divide - by 2)?
> >> >
> > I think the difference is that the parameter in the Amber force field
> files
> > is k from the equation
> >
> > E_bond = k(x-x0)^2
> >
> > whereas in the GROMACS force fields, the force constant is k from the
> > equation
> >
> > E_bond = 1/2 k (x-x0)^2
> >
> > which is the more classical version of Hooke's law since 'k' is the
> actual
> > stiffness of the oscillator.
> >
> > HTH,
> > Jason
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
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PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Received on Tue Mar 26 2013 - 09:30:03 PDT
