From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Oct 15 2013 - 12:44:33 CDT
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?
> 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,
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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