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

Tanping Li jia_11_osu at yahoo.com
Fri Feb 17 20:46:54 CET 2012

Hey Justin,

Really appreciate your help on this. I use the charge of ligand from Gaussian calculation, rather than the charge from PRODRG. It is so good to know that Gromos96+ATB work for my system.


--- On Fri, 2/17/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, February 17, 2012, 2:37 PM
> 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
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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