[gmx-users] Ligand hybridization

[sun]

Use ATB for sure. PRODRG co-ordinates, charges are highly doubtful. I have prepared my ligand's topology using PRODRG and it took me almost 10 days to correct the charges. ATB is pretty good. 

Sent from my iPhone

> On 05-Jul-2016, at 10:26 pm, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> On 7/5/16 10:50 AM, Chetan Puri wrote:
>> I am trying to do a protein- ligand simulation.
>> 
>> And the prodrg server provides the ligand out  put by completely removing
>> the double bonds(making it saturated)
>> 
>> So is there any way to do it.
> 
> See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure you fix the PRODRG topology because the charges won't be right.  Or use a better server like ATB.
> 
> -Justin
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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