[gmx-users] Re: Using new atom types

[Fabian Casteblanco]

Hello Peter C. Lai,

Thanks for your help.  I read your back and forth posts on the GMX
Forums with Mark Abraham.  Is there any way that I can simply use it
from the topology without having to include it on the
charmm27.ff/forcefield.itp?  I have to run this on a cluster and I
don't think I have access to change internal files.  I do not need to
run using pdb2gmx.  Also, how did you manage to include the LJ 1-4
parameters?  Did you have to write out each and every pair on GROMACS?

Thanks for you help.
-Fabian


On Thu, Jul 7, 2011 at 2:16 PM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> wrote:
> 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
> DrugName
>
> [ 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
>



-- 
Best regards,

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