[gmx-users] Query- Ligand parametrization

[Priya Das]

The following is the attached pose.str file.

1) Does param penalty or charge penalty matters?
2) How do we know that the list does not accept attachments?
3) I am following the tutorial for validation of penalties. As CHARMM is
not free cannot download it. So using Accelry's Discovery Studio interface
to perform QM-MM calculations (nstep= 500).

Am i on the right track?

On Mon, Mar 23, 2015 at 8:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/22/15 12:37 PM, Priya Das wrote:
>
>> Dear all,
>>
>> I tried to generate parameters for ligand. I am not well in analyzing the
>> penalty.
>> Seeking advices if i need to further refine the parameters of the attached
>> .str file to reduce the penalty.
>>
>>
>>
> The list doesn't accept attachments (if I had a nickel for every time I've
> said that...)
>
> Penalties are described in the ParamChem FAQ, along with a link to the
> CGenFF tutorial and paper.  That's where you need to get your information.
>
> https://cgenff.paramchem.org/commonFiles/faq.php#validopt
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala