[gmx-users] ATB & SWISSPARAM Topologies

Justin A. Lemkul jalemkul at vt.edu
Tue May 15 12:50:12 CEST 2012

On 5/15/12 5:54 AM, Anirban wrote:
> Hi ALL,
> How accurate are the topologies of non-standard molecules generated by ATB or
> SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to
> carry out manual checks like that required for PRODRG outputs?
> Any suggestion is welcome.

I would always verify parameters before running real production simulations.  I 
believe ATB and SwissParam are, in general, far more reliable than PRODRG, but I 
doubt it can be stated universally that any automated method is inherently flawless.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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