[gmx-users] PRODRG -cgnr

[Justin Lemkul]

On 7/28/14, 8:41 AM, Atila Petrosian wrote:
> Dear Justin
>
> Unfortunately, now I don't access the file-sharing system.
>
> My ligand molecule is in the below link:
>
> http://en.wikipedia.org/wiki/Isoniazid
>
> Please check it.
>

The hydrazide moiety will be your biggest challenge.  While you can piece that 
together from existing amine and amide parameters, I doubt they'll be 
sufficiently accurate.  Moreover, there won't be suitable bonded parameters 
(bonds, angles, and dihedrals) for that moiety in the force field.

-Justin

>
> On Mon, Jul 28, 2014 at 4:53 PM, Atila Petrosian <atila.petrosian at gmail.com>
> wrote:
>
>> Dear Justin
>>
>> Thanks for your answer.
>>
>> I'm beginner in this regard. I'm not sure . I think that my molecule is comprised
>> almost of existing functional groups.
>>
>>   I attached picture of my molecule to this email. please check it.
>>
>> Please help me to do this issue correctly.
>>
>> Thanks for your time and consideration.
>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================