[gmx-users] Query- Ligand parametrization

[Priya Das]

I am sorry to bother again and again.  I am new to it and still learning
the basics.
My molecule is a decahydroquinoline. The paramchem generated .str file is
HERE
<https://cgenff.paramchem.org/initguess/filedownload.php?file=20150328/Pose1.str>
.
I am following CGennFF tutorial and your instructions as HERE
<http://mackerell.umaryland.edu/~kenno/cgenff/program.html>. As penalties
are there i need to use QM, but i am not able to run CHARMM simulations as
CHARMM is not freely available. So tried to use this Toolkit
<http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/>, but still in vain.






On Fri, Mar 27, 2015 at 4:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/15 4:05 AM, Priya Das wrote:
>
>> The following is the attached pose.str file.
>>
>> 1) Does param penalty or charge penalty matters?
>>
>
> Yes.
>
>  2) How do we know that the list does not accept attachments?
>>
>
> It's something I say weekly, if not more often.  It should also have been
> in the welcome email when you subscribed.
>
>  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).
>>
>>
> There is no QM/MM in the parametrization.  There are QM calculations for
> bonded parameter scans, frequency calculations, and water interaction
> energies.  Any MM or MD software that can do single-point energy
> evaluations and geometry optimizations can handle the MM energy part.
> CHARMM is just very easy to use in this case.  You can certainly do the MM
> energy evaluations and optimizations in GROMACS or whatever software you
> like, though it may be a bit laborious.
>
>
> -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