Re: [AMBER] problems in parameters calculated with AMBER

From: Anna Marabotti <>
Date: Tue, 26 Mar 2013 10:41:00 +0100

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 Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Phone: +39 089 969583
Fax: +39 089 969603
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, ha scritto:
> Message: 23
> Date: Mon, 25 Mar 2013 08:27:59 -0400
> From: Jason Swails<>
> Subject: Re: [AMBER] problems in parameters calculated with AMBER
> To: AMBER Mailing List<>
> Message-ID:
> <>
> Content-Type: text/plain; charset=ISO-8859-1
> On Mon, Mar 25, 2013 at 8:12 AM, Anna MARABOTTI<> 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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Received on Tue Mar 26 2013 - 03:00:03 PDT
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