[gmx-users] ATB & SWISSPARAM Topologies

[Anirban]

Thanks a lot Justin!

On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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