[gmx-users] Using new atom types

Fabian Casteblanco fabian.casteblanco at gmail.com
Thu Jul 7 20:16:56 CEST 2011

Hello all,

I'm building a drug molecule using CHARMM parameters.  The thing is
that there is this new CGenFF (an extension of CHARMM, but very
similar to the old CHARMM atom types
http://mackerell.umaryland.edu/~kenno/cgenff/) that uses better
parameters for drug-like molecules.  I would like to use these new
parameters for this drug molecule (pretty big molecule).  I took all
the parameter values from CGenFF and I converted them to values used
by Gromacs and I formatted it just like the original ffcharm27.itp
files found in Gromacs.  The only thing is that when it comes to
Lennard Jones,1-4 parameters, CHARMM gives you the actual individual
value by atom whereas Gromacs has already all the pair listed values
stored.  Is there any way that I can place these 1-4 parameters in the
drug.itp file itself and have Gromacs calculate the combinations just
as it does for the regular LJ values?

I have:
-CgenFFbon.itp   (bonded, angle, dihedral parameters,etc)
-CgenFFnb.itp     (nonbonded LJ values)
-CgenFF.atp        (atom type file)

What exactly do I need to include on my drug.itp (or drug.top) file
inorder so it can read these parameters from the files above?

Thanks for anyones help!  Greatly appreciated!!

;SAMPLE topology:
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

#include "drug.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
DDD                    1

Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com

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