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

[Austin B. Yongye]

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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