[gmx-users] The solvation free energy of a vdw ligand

[Justin A. Lemkul]

Tanping Li wrote:
> Hey Justin,
> 
> Thanks for the help. There is a ligand in my system, whose top file comes
> from the PRODRG package. PRODRG package only gives the ffgmx force field.

There is a newer version of PRODRG that produces Gromos96 43a1 topologies.  The 
quality of PRODRG topologies is generally very poor and thus the topologies 
should be thoroughly refined before they are ever used.  In the absence of 
refinement, we have found, the results are totally unreliable.

http://pubs.acs.org/doi/abs/10.1021/ci100335w

For Gromos96 force fields, a far better topology builder is ATB.

http://compbio.biosci.uq.edu.au/atb/

> Could ffgmx ligand combine protein with other force field? I would be happy
> to transfer to the newer force field if my system allows. Thanks again and
> have a good weekend!
> 

Force fields cannot be mixed and matched (with very limited exceptions).  Choose 
one and stick with it for all elements of your system.  Choosing a proper force 
field that can adequately describe a complex system is not an easy task.  There 
are many options and you should invest considerable time reading about the 
benefits and drawbacks of each.  You should not simply use ffgmx (which is, in 
itself, questionable) just because there is a convenient tool (PRODRG) that is 
also unreliable.  Spending a few hours reading may save you months of effort 
that wind up being wasted.

-Justin

-- 
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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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