From: João Ribeiro KS (
Date: Fri Sep 02 2016 - 09:31:02 CDT

Dear Jrhau,

QwikMD/NAMD or any other MD simulation package will accept the topologies
and parameters that you give (if you respect the file structure).

The parameters will determine the dynamics of the system and therefore the
energies, which means that you will most probably have different affinity

When you say the conformation of the ligand, is this the conformation
present in the crystal structure or is a conformation generated by a
docking software or by a script?



On Fri, Sep 2, 2016 at 9:18 AM jrhau lung <> wrote:

> Dear João:
> Thanks for your prompt reply. Since the Gaussian09 is currently
> unavailable to me, I use CgenFF paramchem webserver to generate the CgenFF
> for my ligand.
> The generated str file show penalty scores for many atoms between 50 to
> 100.
> This is definitely not good enough to initiate a NAMD2 simulation, but
> this parameter could be accepted by QwikMD. Since there is no red highlight
> on the ligand.
> Since the FFTK refinement would change the ligand docking conformation (i
> guess that from the QwikMD ethanol tutorial), does this affect binding
> affinity estimation?
> Thanks,
> sincerely, Jrhau
> 2016-09-02 21:50 GMT+08:00 João Ribeiro <>:
>> Hi,
>> If QwikMD is warning about missing topologies & parameters, you cannot
>> ignore. Either you add the topologies and the parameters for the unknown
>> residue, or you delete the molecule.
>> Regarding the parameters, you can always use the initial guess from
>> CgenFF and refine it with FFTK.
>> Best
>> Joao
>> On Fri, Sep 2, 2016 at 12:21 AM jrhau lung <> wrote:
>>> To simulate the binding affinity between the ligand and receptor, how
>>> should I choose a lignad conformation to generate CgenFF.
>>> My lignad in docking pose receive a higher CgenFF penalty score (between
>>> 50 to 100) than in native pose.
>>> Should I just ignore the warning message in QwikMD or choose a CgenFF
>>> parameter with a much lower penalty score generated from native pose?
>>> Thanks for any suggestion
>>> sincerely,
>>> Jrhau