Re: free energy of binding

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Jul 07 2011 - 17:12:34 CDT

Francesco,

We've implemented "free energy perturbation" and "thermodynamic
integration" methods for problems like yours. The free energy
perturbation tutorial, specifically sections 3 & 4, should help point
you in the right direction.

http://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/tutorial-FEP.pdf
http://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/FEP-tutorial-files.tar.gz

Best,
Chris

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax: 217-244-6078
On Thu, Jul 7, 2011 at 4:50 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> First, I have the systems equilibrated with charmm ff and it would be
> too much work to change to amber ff. Second, the systems have lipids
> and amber ffs are not so good for lipids. Third, the system is based
> on a multimer protein and amber renumbers continuously all atoms,
> unlike charmm that preserves subunits. Examining interactions with
> continuous numbering will be headache. But it was kind from you to
> give details. I wish you success with the method.
> chiendarret
>
> On Thu, Jul 7, 2011 at 5:50 PM, Dong Luo <us917_at_yahoo.com> wrote:
>> AmberTools has utilities to calculate free energy of binding from a single
>> MD trajectories that simulated with Amber force field. NAMD supports Amber
>> force field.
>> I recently did a test with this. It works though I am not sure of the
>> quality of the results because it's the first time for me to calculate the
>> binding free energy.
>> Briefly the steps are:
>> 1. Convert pdb file to Amber friendly format according to AmberTools'
>> manual. The online tool:
>> http://glycam.ccrc.uga.edu/ccrc/GlycamLITE/Protein/uploadIndex.jsp?option=ff99
>> can help with it.
>> 2. Using AmberTools' tleap to create parameter and coordinates input files
>> for MD. Again check with the manual.
>> 3. Edit NAMD configuration file to use the Amber force field. Check NAMD's
>> guide.
>> 4. Run the simulation.
>> 5. Calculate the free energy of binding following corresponding steps in the
>> Amber tutorial:
>> http://ambermd.org/tutorials/advanced/tutorial3/
>> Dong
>>
>> ________________________________
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> To: NAMD <namd-l_at_ks.uiuc.edu>
>> Sent: Thursday, July 7, 2011 5:52 AM
>> Subject: namd-l: free energy of binding
>>
>> How could free energy of binding of a small-molecule ligand to a
>> protein receptor be calculated from namd md trajectories?
>> Is there a validated specific procedure for namd, or should a
>> literature method be imitated? For example Åqvist's method:
>>
>> Åqvist, J., Medina, C., and Samuelsson, J. E. (1994) A new
>> method for predicting binding affinity in computer-aided drug design.
>> Protein Eng. 7, 385–391.
>>
>> thanks for sharing experience on this hot topic
>>
>> francesco pietra
>>
>>
>>
>>
>
>

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