[gmx-users] Query- Ligand parametrization

[Justin Lemkul]

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

-- 
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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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