[gmx-users] free energy perturbation

[Justin A. Lemkul]

antonio wrote:
> Dear gromacs users
> I am trying to carry out a free energy perturbation to evaluate the
> difference in binding energy between two inhibitors of the same protein.
> I have read a lot of post but i did no understand how to create the
> topology file.
> have i to write a mixed pdb of the two inhibitors structure modifying
> the value of beta factor to -1;0,1 for disappearing and rising atoms and
> than to proceed by pdb2gmx ?
> Could someone please link a tutorial or a guide to follow.

Please see the manual, section 5.7.4 "Topologies for free energy calculations," 
which includes a relevant example of a topology for transforming between two 
molecules.  There have been significant changes to the free energy code since 
version 3.3.3, when this type of transformation was (almost) completely 
controlled in the topology, so your mileage may vary.

You do not want (or need) a "mixed" .pdb file.  The B-factor field is irrelevant 
for such applications, and a hybrid structure will probably break pdb2gmx, anyway.

-Justin

> thanks in advance
> Antonio  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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