VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Fri Sep 02 2016 - 09:17:59 CDT

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 <jrvribeiro_at_gmail.com>:

> 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 <jrhaulung_at_gmail.com> 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
>>
>