Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity

From: Jason Swails <>
Date: Sat, 5 Feb 2011 14:47:11 -0500


On Sat, Feb 5, 2011 at 2:13 AM, Sangita Kachhap <>wrote:

> Hello all
> I want to study the effect of perticular water molecule on affinity and
> specificity
> of protien DNA binding.
> As these can be define by standared free energy change I thought,if I can
> calculate the
> standared free energy change of protein - DNA interaction
> 1)considering that perticular water molecule in interaction
> 2)In absence of that perticular water molecule
> Then the effect of water molecule in affinty and specificity can be define.
> So I thought to use MMPBSA but it runs implicit and I am not getting how to
> include
> that perticular water molecule in calculation of standared free energy
> change.
> Can anyone please suggest is it possible and how to do it?

You can still use MM/PBSA. If you use, you will have to
preprocess the trajectory and strip out all of the waters that you don't
want to include (just the one that you do). Check out the "closest" command
in ptraj. After this, just set "strip_mdcrd = 0" to prevent the script from
stripping bulk solvent and include the water molecule in either the receptor
or ligand topology files. Note that MMPBSA still uses an implicit solvent
model (which I think is what you want), but still treats that one important
water molecule explicitly.

You can do decomposition analysis to aid in looking at specific

Hope this helps,

> With regard
> Sangita Kachhap
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Feb 05 2011 - 12:00:04 PST
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