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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 19 16:08:56 CEST 2011


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 
> <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-CP10.100.0-3.Dimethyl phosphate
>
> 1-0.500.0-2.
>
> 10.100.01
>

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110720/e7f96fcd/attachment.html>


More information about the gromacs.org_gmx-users mailing list