[gmx-users] Conversion of the GLYCAM dihedral parameters
sa
sagmx.mail at gmail.com
Thu Jul 21 11:48:53 CEST 2011
>
> Yeah I have also found this page. Finally I did the conversion. I am
> currently testing the parameters.
>
Thank you Austin and Mark for your help
SA-
>
> ------------------------------
>
> Message: 4
> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
> From: "Austin B. Yongye" <ybausty at yahoo.com>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
> in the GROMACS format.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <1311171438.14853.YahooMailClassic at web161422.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> > So my questions are: how to convert it in the gromacs format ?
> I haven't done AMBER to GROMACS conversions. But a google search led me to
> this page. It's just a matter of knowing the different formats.
>
> http://ffamber.cnsm.csulb.edu
>
> > Is it correct to use the absolute value of the multiplicity in my
> parameters and use the negative values of barrier heights when they are
> exist in the AMBER parameters? Since, I have noticed that in the AMBER
> ff port in GROMACS, the multiplicity values are always set to > 0
> and the barrier heights have sometime a negative value.
>
>
>
> So my questions are: how to convert it in the gromacs format ? Is it
> correct to use the absolute value of the multiplicity in my parameters and
> use the negative values of barrier heights when they are exist in the AMBER
> parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the
> multiplicity values are always set to > 0 and the barrier heights have
> sometime a negative value.
>
>
> Thank you again for your advice.
>
> SA-
>
>
>
>
> Message: 1
>
> Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
>
> From: "Austin B. Yongye" <ybausty at yahoo.com>
>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
>
> in the GROMACS format.
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> Message-ID:
>
> <1311098935.93905.YahooMailClassic at web161426.mail.bf1.yahoo.com>
>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> It is normal to have combinations of negative and positive values for the
> barrier heights. Those are just the best coefficients to reproduce some QM
> rotational energy curve during the parameterization. The negative
> periodicities are a convention from AMBER. They simply indicate that the
> dihedral angle potential has more than one term. For your example below:
>
>
>
>
> O2-P
>
> -OS-CP 1 0.10 0.0 -3. Dimethyl
> phosphate
>
> 1 -0.50 0.0 -2.
>
>
>
> 1 0.10
>
> 0.0 1
>
> -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive
> value is reached, terms for the O2-P-OS-CP potential have been completely
> accounted for.
>
>
>
> Hope that helps.
>
> Austin-
>
>
>
>
>
> --- On Tue, 7/19/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
>
>
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in
> the GROMACS format.
>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>
> Date: Tuesday, July 19, 2011, 7:08 AM
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 19/07/2011 11:56 PM, sa wrote:
>
>
>
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>
>
> Dear
>
> GROMCS users,
>
>
>
> I
>
> am trying to convert some GLYCAM parameters in GROMACS format.
>
> For this
>
> purpose, I am using the latest GLYCAM parameters downloaded
>
> from the RJ. Woods’
>
> website and the examples given in the acpype code (here for
>
> the dihedral angles) :
>
>
>
>
>
>
>
>
>
>
>
>
> http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1
>
>
>
>
>
>
>
>
>
>
>
>
> -------------------
>
> # dihedral idivf barrier hight/2 kcal/mol phase degrees
> periodicity comments
>
> X -ca-ca-X 4 14.500* 180.000
> 2.000 intrpol.bsd.on C6H6
>
>
>
> * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in
> topolbuild, why?) = 30.334 or 15.167 kJ/mol
>
> # X -CA-CA-X 4 14.50 180.0 2.
> intrpol.bsd.on C6H6 (from parm99.dat)
>
>
>
> # X-CA-CA-X 3 30.33400 0.00000 -30.33400 0.00000
> 0.00000 0.00000 ; intrpol.bsd.on C6H6
>
>
>
> -----------
>
>
>
> I have no problems with the parameters for proteins. But, in case of
> the GLYCAM parameters, I am a little confused
>
>
>
> about the conversion of dihedral force constants (DFC), especially when the
> DFC and the periodicity values are < 0 for example
>
> for this torsion:
>
>
>
>
>
> O2-P
>
> -OS-CP 1 0.10 0.0 -3. Dimethyl
> phosphate
>
> 1 -0.50 0.0 -2.
>
>
>
> 1 0.10
>
> 0.0 1
>
>
>
>
>
>
>
> Where only a positive value makes sense, sometimes people use
>
> negative values to indicate some special functional form. This can
>
> be easier to code. Regardless, you'll have to check out the GLYCAM
>
> documentation and see what is meant, before you can address how to
>
> convert it into a GROMACS format. Obviously the contents of parts of
>
> chapter 4 and 5 of the manual will be important.
>
>
>
>
>
>
>
> Mark
>
>
>
>
>
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>
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