On Wed, Oct 28, 2015 at 11:02 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
> Dear All,
>
> I have a question about using different parameter files for nonbonded
> interactions. My simulation consists of two identical sugar molecules in
> explicit water solvent. I parametrize them with Glycam06 force field and
> I use TIP3P for the water model. I am experimenting on Glycam force
> field, especially on sugar-sugar nonbonded interactions.
>
> I want to define nonbonded interactions between sugar molecules with the
> modified field, but I want to keep sugar-water interaction as they are
> in Glycam. I wanted to know if there is a way to do this in Leap
> directly, or should I consult to ParmEd for modifying the topology file?
>
You can do it in LEaP directly with an LJEDIT section, but this is new
functionality that is not documented (I *think* I know how it works, but
I'm not positive).
My suggestion is to use "changeLJPair" in ParmEd and use that to play with
different values and optimize your model. Once you have the final
parameters you want, then add the corresponding LJEDIT section to your
frcmod file.
If you do it this way, then you can always validate your frcmod file with
the LJEDIT sections against the answers you know to be correct generated by
ParmEd.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 28 2015 - 19:00:03 PDT
