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

[Austin B. Yongye]

> 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:





















      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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