From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Oct 15 2013 - 15:05:11 CDT
Thanks all for suggestion!
Now I should find some MM/PBSA tutorials suitable for NAMD/Gromacs
trajectories inputs .
James
2013/10/15 Thomas Evangelidis <tevang3_at_gmail.com>
> You neglect completely the entropic effect of ligand binding:
> DeltaG=DeltaH-T*DeltaS
> Judging from your interaction energy DeltaH ~ 0 so in order to have a
> favourable Free Energy of Binding (DeltaG<0) then DeltaS>0, which means the
> removal of waters and/or ions from the binding cavity by the ligand
> increases the entropy of the system.
>
> As Aron & Kenno suggested, MM/PBSA calculations are most suitable for your
> case. FEP and TI are cumbersome and used more for ligand optimization.
>
>
> On 15 October 2013 21:43, James Starlight <jmsstarlight_at_gmail.com> wrote:
>
>> Aron,
>>
>> thanks for reference.
>>
>> By the way how the Namd-energy plugin could be effectively used ? In case
>> of small tutorial I choce two selections- all atoms of my ligands and 5
>> polar residues surrounded ligand within the protein cavity. Than I
>> calculate electrostatic energy using cutoff and switch values from the conf
>> file of MD production run. In the resulting graph I've obtain Zero-line of
>> the energy during of all simulation run (so if this is POTENTIAL energy it
>> indicate that no interactions between ligand and selected residues have
>> been occurred during MD that is incorect). What I did wrong?
>>
>> James
>>
>>
>> 2013/10/15 Aron Broom <broomsday_at_gmail.com>
>>
>>> there was in fact one recently posted on the NAMD website and mentioned
>>> on the mailing list.
>>>
>>>
>>> On Tue, Oct 15, 2013 at 1:42 PM, James Starlight <jmsstarlight_at_gmail.com
>>> > wrote:
>>>
>>>> So in that case just ussage of VMD's NAMD energy module would give
>>>> wrong results of the G-bonding estimation.
>>>> Also I've found that Free energy perturbation and Thermodynamic
>>>> integration could be usefull for affinity measurements. I've seen tutorials
>>>> for implementation of such methods for gromacs and charm but is there any
>>>> for NAMD?
>>>>
>>>> James
>>>>
>>>>
>>>> 2013/10/15 Aron Broom <broomsday_at_gmail.com>
>>>>
>>>>> As an FYI, that energy is going to be border-line useless without
>>>>> having an unbound control to subtract.
>>>>>
>>>>> You may want to read up on the literature surrounding this, it is a
>>>>> very large topic, with many nice reviews, and the problem itself is fairly
>>>>> nuanced. What you seem to be talking about is an MM/PBSA style of
>>>>> calculation, so I'd start by looking into that.
>>>>>
>>>>>
>>>>> On Mon, Oct 14, 2013 at 2:20 PM, James Starlight <
>>>>> jmsstarlight_at_gmail.com> wrote:
>>>>>
>>>>>> Dear NAMD users,
>>>>>>
>>>>>>
>>>>>> I have trajectory of the protein complexed with the ligand (burried
>>>>>> in the protrein interiour from the start of simulation). Now I want to find
>>>>>> out how I can calculate affinity of my ligand to the protein. The one
>>>>>> possible way of do such task is the interaction energy estimation of my
>>>>>> complex (based on the occurence of the non-covalent contacts between both
>>>>>> partners during production run). Could someone provide me with some
>>>>>> tutorial or explain me how I could perform such analysis with the VMD tools
>>>>>> ?
>>>>>>
>>>>>> Thanks for help,
>>>>>>
>>>>>> James
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Aron Broom M.Sc
>>>>> PhD Student
>>>>> Department of Chemistry
>>>>> University of Waterloo
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang_at_pharm.uoa.gr
>
> tevang3_at_gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:46 CST