VMD-L Mailing List

From: Seth Axen (seth.axen_at_gmail.com)
Date: Sat May 21 2016 - 00:02:24 CDT

You'll want to look into the CGenFF, the CHARMM General Forcefield. If you
submit your molecule to ParamChem.org, it will assign any missing
parameters by analogy and provide a penalty to indicate how good the
analogy is. But you'll want to make sure you have the right protonation
state of your molecule at the pH of your simulation. It looks like for the
protonated form, all necessary parameters are in CGenFF, whereas for the
unprotonated form, you may need to do some refinement.
Seth

On Fri, May 20, 2016 at 5:29 PM Natnael Doilicho <nbd_at_uchicago.edu> wrote:

> Hi All,
>
> I'm looking for CHARMM-compatible forcefield parameters for the molecule
> HS(CH2)11NH2, a sulfur attached to a longish alkane chain terminated by
> NH2.
>
> Does anyone know where I can find such parameters or perhaps similar
> parameters that analogize closely, like de-protinated L-Lysine?
>
> Best,
>
> *Natnael B. Doilicho *
>
>
>