[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.

[sa]

Thank you Austin, for the clarification,

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:
>
>
>
>
>
>
>
>
>
>
>      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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